[liggghts] branch master updated (19039b2 -> f01a307)
Anton Gladky
gladk at moszumanska.debian.org
Thu Mar 6 19:43:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch master
in repository liggghts.
from 19039b2 Update changelog.
adds c18713f Imported Upstream version 2.3.8
adds 76193e3 Imported Upstream version 3.0.0
new 32191e2 Merge.
new f92bd70 Update patch.
new 7f92ad9 Update changelog.
new f01a307 Minor fix.
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
README | 0
bench/GPU/README | 6 +-
bench/GPU/in.rhodo.cuda | 2 +-
bench/log.30Jul13.chain.fixed.linux.1 | 59 +
bench/log.30Jul13.chain.fixed.linux.4 | 59 +
bench/log.30Jul13.chain.scaled.linux.4 | 75 +
bench/log.30Jul13.chute.fixed.linux.1 | 63 +
bench/log.30Jul13.chute.fixed.linux.4 | 63 +
bench/log.30Jul13.chute.scaled.linux.4 | 73 +
bench/log.30Jul13.eam.fixed.linux.1 | 67 +
bench/log.30Jul13.eam.fixed.linux.4 | 67 +
bench/log.30Jul13.eam.scaled.linux.4 | 67 +
bench/log.30Jul13.lj.fixed.linux.1 | 64 +
bench/log.30Jul13.lj.fixed.linux.4 | 64 +
bench/log.30Jul13.lj.scaled.linux.4 | 64 +
bench/log.30Jul13.rhodo.fixed.linux.1 | 99 +
bench/log.30Jul13.rhodo.fixed.linux.4 | 99 +
bench/log.30Jul13.rhodo.scaled.linux.4 | 120 +
bench/log.9Jan12.chain.fixed.linux.1 | 59 -
bench/log.9Jan12.chain.fixed.linux.4 | 59 -
bench/log.9Jan12.chain.scaled.linux.4 | 75 -
bench/log.9Jan12.chute.fixed.linux.1 | 63 -
bench/log.9Jan12.chute.fixed.linux.4 | 63 -
bench/log.9Jan12.chute.scaled.linux.4 | 73 -
bench/log.9Jan12.eam.fixed.linux.1 | 67 -
bench/log.9Jan12.eam.fixed.linux.4 | 67 -
bench/log.9Jan12.eam.scaled.linux.4 | 67 -
bench/log.9Jan12.lj.fixed.linux.1 | 64 -
bench/log.9Jan12.lj.fixed.linux.4 | 64 -
bench/log.9Jan12.lj.scaled.linux.4 | 64 -
bench/log.9Jan12.rhodo.fixed.linux.1 | 98 -
bench/log.9Jan12.rhodo.fixed.linux.4 | 98 -
bench/log.9Jan12.rhodo.scaled.linux.4 | 119 -
couple/README | 38 -
couple/fortran/README | 9 -
couple/fortran/libfwrapper.c | 129 -
couple/lammps_quest/Makefile.g++ | 47 -
couple/lammps_quest/README | 64 -
couple/lammps_quest/in.lammps | 20 -
couple/lammps_quest/lmpqst.cpp | 262 -
couple/lammps_spparks/README | 71 -
couple/lammps_spparks/image.lammps.1.png | Bin 286212 -> 0 bytes
couple/lammps_spparks/image.lammps.10.png | Bin 329034 -> 0 bytes
couple/lammps_spparks/image.lammps.20.png | Bin 337285 -> 0 bytes
couple/lammps_spparks/image.spparks.1.png | Bin 266049 -> 0 bytes
couple/lammps_spparks/image.spparks.10.png | Bin 234933 -> 0 bytes
couple/lammps_spparks/image.spparks.20.png | Bin 267721 -> 0 bytes
couple/simple/README | 78 -
couple/simple/in.lj | 24 -
couple/simple/simple.c | 116 -
couple/simple/simple.cpp | 121 -
couple/simple/simple.f90 | 135 -
debian/changelog | 6 +
debian/control | 8 +-
.../{libliggghts2.install => libliggghts3.install} | 0
debian/patches/01_add_cmake_files.patch | 94 +-
debian/rules | 2 +-
doc/Developer.pdf | Bin 0 -> 85778 bytes
doc/Eqs/angle_fourier.jpg | Bin 0 -> 4618 bytes
doc/Eqs/angle_fourier.tex | 9 +
doc/Eqs/angle_fourier_simple.jpg | Bin 0 -> 2761 bytes
doc/Eqs/angle_fourier_simple.tex | 9 +
doc/Eqs/angle_quartic.jpg | Bin 0 -> 5273 bytes
doc/Eqs/angle_quartic.tex | 9 +
doc/Eqs/compute_msd_nongauss.jpg | Bin 0 -> 7277 bytes
doc/Eqs/compute_msd_nongauss.tex | 9 +
doc/Eqs/dihedral_fourier.jpg | Bin 0 -> 4544 bytes
doc/Eqs/dihedral_fourier.tex | 9 +
doc/Eqs/dihedral_nharmonic.jpg | Bin 0 -> 3231 bytes
doc/Eqs/dihedral_nharmonic.tex | 9 +
doc/Eqs/dihedral_quadratic.jpg | Bin 0 -> 2067 bytes
doc/Eqs/dihedral_quadratic.tex | 9 +
doc/Eqs/dihedral_sign.jpg | Bin 0 -> 19297 bytes
doc/Eqs/eff_ECP1.jpg | Bin 0 -> 5146 bytes
doc/Eqs/eff_ECP1.tex | 9 +
doc/Eqs/eff_ECP2.jpg | Bin 0 -> 9744 bytes
doc/Eqs/eff_ECP2.tex | 8 +
doc/Eqs/fix_gld1.jpg | Bin 0 -> 14274 bytes
doc/Eqs/fix_gld1.tex | 13 +
doc/Eqs/fix_lb_fluid_boltzmann.jpg | Bin 0 -> 4643 bytes
doc/Eqs/fix_lb_fluid_boltzmann.tex | 14 +
doc/Eqs/fix_lb_fluid_fluidforce.jpg | Bin 0 -> 2358 bytes
doc/Eqs/fix_lb_fluid_fluidforce.tex | 14 +
doc/Eqs/fix_lb_fluid_gammadefault.jpg | Bin 0 -> 4793 bytes
doc/Eqs/fix_lb_fluid_gammadefault.tex | 14 +
doc/Eqs/fix_lb_fluid_navierstokes.jpg | Bin 0 -> 9311 bytes
doc/Eqs/fix_lb_fluid_navierstokes.tex | 16 +
doc/Eqs/fix_lb_fluid_properties.jpg | Bin 0 -> 3471 bytes
doc/Eqs/fix_lb_fluid_properties.tex | 17 +
doc/Eqs/fix_lb_fluid_stress.jpg | Bin 0 -> 2530 bytes
doc/Eqs/fix_lb_fluid_stress.tex | 14 +
doc/Eqs/fix_lb_fluid_viscosity.jpg | Bin 0 -> 6522 bytes
doc/Eqs/fix_lb_fluid_viscosity.tex | 14 +
doc/Eqs/fix_ti_rs_force.jpg | Bin 0 -> 1777 bytes
doc/Eqs/fix_ti_rs_force.tex | 11 +
doc/Eqs/fix_ti_rs_function_1.jpg | Bin 0 -> 2534 bytes
doc/Eqs/fix_ti_rs_function_1.tex | 9 +
doc/Eqs/fix_ti_rs_function_2.jpg | Bin 0 -> 3233 bytes
doc/Eqs/fix_ti_rs_function_2.tex | 9 +
doc/Eqs/fix_ti_rs_function_3.jpg | Bin 0 -> 4801 bytes
doc/Eqs/fix_ti_rs_function_3.tex | 9 +
doc/Eqs/fix_ti_spring_force.jpg | Bin 0 -> 3627 bytes
doc/Eqs/fix_ti_spring_force.tex | 11 +
doc/Eqs/fix_ti_spring_function_1.jpg | Bin 0 -> 1040 bytes
doc/Eqs/fix_ti_spring_function_1.tex | 9 +
doc/Eqs/fix_ti_spring_function_2.jpg | Bin 0 -> 5753 bytes
doc/Eqs/fix_ti_spring_function_2.tex | 9 +
doc/Eqs/fix_wall_colloid.jpg | Bin 18572 -> 17879 bytes
doc/Eqs/fix_wall_colloid.tex | 2 +-
doc/Eqs/fix_wall_lj1043.jpg | Bin 0 -> 10996 bytes
doc/Eqs/fix_wall_lj1043.tex | 12 +
doc/Eqs/improper_cossq.jpg | Bin 0 -> 2995 bytes
doc/Eqs/improper_cossq.tex | 9 +
doc/Eqs/improper_fourier.jpg | Bin 0 -> 4746 bytes
doc/Eqs/improper_fourier.tex | 9 +
doc/Eqs/improper_ring.jpg | Bin 0 -> 11101 bytes
doc/Eqs/improper_ring.tex | 12 +
doc/Eqs/pair_bop.jpg | Bin 0 -> 13202 bytes
doc/Eqs/pair_bop.tex | 9 +
doc/Eqs/pair_comb1.jpg | Bin 15231 -> 19008 bytes
doc/Eqs/pair_comb1.tex | 11 +-
doc/Eqs/pair_comb2.jpg | Bin 17322 -> 40980 bytes
doc/Eqs/pair_comb2.tex | 22 +-
doc/Eqs/pair_coul_dsf.jpg | Bin 0 -> 12261 bytes
doc/Eqs/pair_coul_dsf.tex | 10 +
doc/Eqs/pair_gauss.jpg | Bin 2849 -> 2835 bytes
doc/Eqs/pair_gauss.tex | 4 +-
doc/Eqs/pair_gromacs.jpg | Bin 17058 -> 50447 bytes
doc/Eqs/pair_gromacs.tex | 5 +-
doc/Eqs/pair_meam_spline.jpg | Bin 5555 -> 10530 bytes
doc/Eqs/pair_meam_sw_spline.jpg | Bin 0 -> 17215 bytes
doc/Eqs/pair_meam_sw_spline.tex | 23 +
doc/Eqs/pair_mie.jpg | Bin 0 -> 4686 bytes
doc/Eqs/pair_mie.tex | 10 +
doc/Eqs/pair_mie2.jpg | Bin 0 -> 6502 bytes
doc/Eqs/pair_mie2.tex | 9 +
doc/Eqs/pair_nb3b_harmonic.jpg | Bin 0 -> 1918 bytes
doc/Eqs/pair_nb3b_harmonic.tex | 9 +
doc/Eqs/pair_nm.jpg | Bin 0 -> 6304 bytes
doc/Eqs/pair_nm.tex | 10 +
doc/Eqs/pair_tersoff.jpg | Bin 0 -> 36139 bytes
doc/Eqs/pair_tersoff_mod.jpg | Bin 0 -> 91727 bytes
doc/Eqs/pair_tersoff_mod.tex | 24 +
doc/Eqs/pair_zbl.jpg | Bin 0 -> 32209 bytes
doc/Eqs/pair_zbl.tex | 11 +
doc/JPG/rhodo_staggered.jpg | Bin 0 -> 42303 bytes
doc/Manual.html | 65 +-
doc/Manual.txt | 59 +-
doc/PDF/PDLammps_VES.pdf | Bin 0 -> 65659 bytes
doc/PDF/colvars-refman-lammps.pdf | Bin 0 -> 599768 bytes
doc/PDF/kspace.pdf | Bin 0 -> 158427 bytes
doc/Scripts/correlate.py | 2 +-
doc/Section_accelerate.html | 234 +-
doc/Section_accelerate.txt | 229 +-
doc/Section_commands.html | 330 +-
doc/Section_commands.txt | 241 +-
doc/Section_errors.html | 1481 +-
doc/Section_errors.txt | 1481 +-
doc/Section_example.html | 55 +-
doc/Section_example.txt | 55 +-
doc/Section_gran_models.html | 51 +
doc/Section_gran_models.txt | 46 +
doc/Section_howto.html | 640 +-
doc/Section_howto.txt | 606 +-
doc/Section_intro.html | 17 +-
doc/Section_intro.txt | 19 +-
doc/Section_modify.html | 116 +-
doc/Section_modify.txt | 114 +-
doc/Section_packages.html | 138 +-
doc/Section_packages.txt | 137 +-
doc/Section_python.html | 643 +-
doc/Section_python.txt | 611 +-
doc/Section_start.html | 447 +-
doc/Section_start.txt | 447 +-
doc/Section_tools.html | 106 +-
doc/Section_tools.txt | 106 +-
doc/USER/atc/man_add_molecule.html | 59 +
doc/USER/atc/man_add_species.html | 59 +
doc/USER/atc/man_atom_element_map.html | 58 +-
doc/USER/atc/man_atom_weight.html | 61 +
doc/USER/atc/man_atomic_charge.html | 51 +
doc/USER/atc/man_boundary.html | 48 +
doc/USER/atc/man_boundary_dynamics.html | 46 +
doc/USER/atc/man_boundary_faceset.html | 47 +
doc/USER/atc/man_boundary_integral.html | 61 +-
doc/USER/atc/man_consistent_fe_initialization.html | 51 +
doc/USER/atc/man_contour_integral.html | 62 +-
doc/USER/atc/man_control.html | 72 +
doc/USER/atc/man_control_momentum.html | 68 +
doc/USER/atc/man_control_thermal.html | 76 +
..._control_thermal_correction_max_iterations.html | 53 +
doc/USER/atc/man_decomposition.html | 55 +
doc/USER/atc/man_disp_control.html | 40 -
doc/USER/atc/man_electron_integration.html | 66 +-
doc/USER/atc/man_equilibrium_start.html | 56 +-
doc/USER/atc/man_extrinsic_exchange.html | 54 +-
doc/USER/atc/man_fe_md_boundary.html | 50 +
doc/USER/atc/man_filter_scale.html | 63 +-
doc/USER/atc/man_filter_type.html | 51 +
doc/USER/atc/man_fix_atc.html | 339 +-
doc/USER/atc/man_fix_flux.html | 61 +-
doc/USER/atc/man_fix_nodes.html | 65 +-
doc/USER/atc/man_hardy_computes.html | 85 +-
doc/USER/atc/man_hardy_fields.html | 109 +-
doc/USER/atc/man_hardy_gradients.html | 67 +-
doc/USER/atc/man_hardy_kernel.html | 81 +-
doc/USER/atc/man_hardy_on_the_fly.html | 74 +-
doc/USER/atc/man_hardy_rates.html | 69 +-
doc/USER/atc/man_hardy_set.html | 27 -
doc/USER/atc/man_initial.html | 60 +-
doc/USER/atc/man_internal_atom_integrate.html | 40 +
doc/USER/atc/man_internal_element_set.html | 52 +
doc/USER/atc/man_internal_quadrature.html | 55 +-
doc/USER/atc/man_kernel_function.html | 64 +
doc/USER/atc/man_localized_lambda.html | 48 +
doc/USER/atc/man_lumped_lambda_solve.html | 47 +
doc/USER/atc/man_mask_direction.html | 47 +
doc/USER/atc/man_mass_matrix.html | 51 +
doc/USER/atc/man_material.html | 49 +
doc/USER/atc/man_mesh_add_to_nodeset.html | 51 +
doc/USER/atc/man_mesh_create.html | 56 +
doc/USER/atc/man_mesh_create_elementset.html | 52 +
doc/USER/atc/man_mesh_create_faceset_box.html | 54 +
doc/USER/atc/man_mesh_create_faceset_plane.html | 54 +
doc/USER/atc/man_mesh_create_nodeset.html | 51 +
doc/USER/atc/man_mesh_delete_elements.html | 55 +-
doc/USER/atc/man_mesh_elemset.html | 25 -
doc/USER/atc/man_mesh_faceset.html | 25 -
doc/USER/atc/man_mesh_nodeset.html | 25 -
doc/USER/atc/man_mesh_nodeset_to_elementset.html | 53 +
doc/USER/atc/man_mesh_output.html | 53 +-
doc/USER/atc/man_mesh_quadrature.html | 51 +
doc/USER/atc/man_mesh_read.html | 52 +
doc/USER/atc/man_mesh_write.html | 50 +
doc/USER/atc/man_momentum_time_integration.html | 60 +
doc/USER/atc/man_neighbor_reset_frequency.html | 25 -
doc/USER/atc/man_output.html | 63 +
doc/USER/atc/man_output_elementset.html | 54 +
doc/USER/atc/man_output_nodeset.html | 55 +
doc/USER/atc/man_pair_interactions.html | 50 +
doc/USER/atc/man_poisson_solver.html | 53 +
doc/USER/atc/man_read_restart.html | 58 +-
doc/USER/atc/man_remove_molecule.html | 54 +
doc/USER/atc/man_remove_source.html | 59 +-
doc/USER/atc/man_remove_species.html | 54 +
.../atc/man_reset_atomic_reference_positions.html | 49 +
doc/USER/atc/man_reset_time.html | 65 +
doc/USER/atc/man_sample_frequency.html | 52 +
doc/USER/atc/man_set.html | 56 +
doc/USER/atc/man_source.html | 60 +-
doc/USER/atc/man_source_integration.html | 46 +
doc/USER/atc/man_temperature_definition.html | 47 +
doc/USER/atc/man_thermal_control.html | 47 -
doc/USER/atc/man_thermal_time_integration.html | 59 +
doc/USER/atc/man_time_filter.html | 66 +-
doc/USER/atc/man_time_integration.html | 23 -
doc/USER/atc/man_track_displacement.html | 48 +
doc/USER/atc/man_transfer_atomic_output.html | 27 -
doc/USER/atc/man_transfer_boundary.html | 25 -
doc/USER/atc/man_transfer_internal.html | 25 -
doc/USER/atc/man_transfer_output.html | 31 -
doc/USER/atc/man_unfix_flux.html | 60 +-
doc/USER/atc/man_unfix_nodes.html | 60 +-
doc/USER/atc/man_write_atom_weights.html | 53 +
doc/USER/atc/man_write_restart.html | 58 +-
doc/angle_fourier.html | 77 +
doc/angle_fourier.txt | 71 +
doc/angle_fourier_simple.html | 76 +
doc/angle_fourier_simple.txt | 70 +
doc/angle_quartic.html | 83 +
doc/angle_quartic.txt | 77 +
doc/atom_style.html | 81 +-
doc/atom_style.txt | 81 +-
doc/body.html | 163 +
doc/body.txt | 154 +
doc/bond_quartic.html | 2 +-
doc/bond_quartic.txt | 2 +-
doc/box.html | 69 +
doc/box.txt | 61 +
doc/change_box.html | 12 +-
doc/change_box.txt | 12 +-
doc/communicate.html | 39 +-
doc/communicate.txt | 39 +-
doc/compute.html | 9 +-
doc/compute.txt | 9 +-
doc/compute_angle_local.html | 5 +-
doc/compute_angle_local.txt | 5 +-
doc/compute_atom_molecule.html | 2 +-
doc/compute_atom_molecule.txt | 2 +-
doc/compute_basal_atom.html | 82 +
doc/compute_basal_atom.txt | 76 +
doc/compute_body_local.html | 99 +
doc/compute_body_local.txt | 89 +
doc/compute_bond_local.html | 17 +-
doc/compute_bond_local.txt | 17 +-
doc/compute_coord_atom.html | 79 +-
doc/compute_coord_atom.txt | 80 +-
doc/compute_dihedral_local.html | 5 +-
doc/compute_dihedral_local.txt | 5 +-
doc/compute_displace_atom.html | 32 +-
doc/compute_displace_atom.txt | 32 +-
doc/compute_erotate_sphere_atom.html | 58 +
doc/compute_erotate_sphere_atom.txt | 53 +
doc/compute_group_group.html | 108 +-
doc/compute_group_group.txt | 105 +-
doc/compute_gyration.html | 21 +-
doc/compute_gyration.txt | 21 +-
doc/compute_gyration_molecule.html | 37 +-
doc/compute_gyration_molecule.txt | 34 +-
doc/compute_improper_local.html | 5 +-
doc/compute_improper_local.txt | 5 +-
doc/compute_inertia_molecule.html | 83 +
doc/compute_inertia_molecule.txt | 78 +
doc/compute_ke.html | 10 +-
doc/compute_ke.txt | 10 +-
doc/compute_msd.html | 41 +-
doc/compute_msd.txt | 41 +-
doc/compute_msd_nongauss.html | 90 +
doc/compute_msd_nongauss.txt | 80 +
doc/compute_pe.html | 10 +-
doc/compute_pe.txt | 10 +-
doc/compute_pe_atom.html | 3 +-
doc/compute_pe_atom.txt | 3 +-
doc/compute_property_atom.html | 35 +-
doc/compute_property_atom.txt | 35 +-
doc/compute_property_local.html | 18 +-
doc/compute_property_local.txt | 18 +-
doc/compute_rdf.html | 42 +-
doc/compute_rdf.txt | 41 +-
doc/compute_reduce.html | 2 +-
doc/compute_reduce.txt | 2 +-
doc/compute_slice.html | 2 +-
doc/compute_slice.txt | 2 +-
doc/compute_stress_atom.html | 16 +-
doc/compute_stress_atom.txt | 15 +-
doc/compute_temp_asphere.html | 5 +
doc/compute_temp_asphere.txt | 5 +
doc/compute_temp_deform.html | 15 +
doc/compute_temp_deform.txt | 15 +
doc/compute_temp_profile.html | 83 +-
doc/compute_temp_profile.txt | 79 +-
doc/compute_temp_region.html | 12 +-
doc/compute_temp_region.txt | 12 +-
doc/compute_ti.html | 35 +-
doc/compute_ti.txt | 35 +-
doc/compute_voronoi_atom.html | 162 +
doc/compute_voronoi_atom.txt | 152 +
doc/delete_atoms.html | 16 +-
doc/delete_atoms.txt | 16 +-
doc/delete_bonds.html | 23 +-
doc/delete_bonds.txt | 23 +-
doc/dihedral_coeff.html | 9 +
doc/dihedral_coeff.txt | 9 +
doc/dihedral_fourier.html | 81 +
doc/dihedral_fourier.txt | 76 +
doc/dihedral_harmonic.html | 13 +
doc/dihedral_harmonic.txt | 13 +
doc/dihedral_nharmonic.html | 78 +
doc/dihedral_nharmonic.txt | 72 +
doc/dihedral_quadratic.html | 77 +
doc/dihedral_quadratic.txt | 72 +
doc/dihedral_style.html | 36 +-
doc/dihedral_style.txt | 38 +-
doc/dimension.html | 2 +-
doc/dimension.txt | 2 +-
doc/displace_atoms.html | 34 +-
doc/displace_atoms.txt | 35 +-
doc/dump.html | 166 +-
doc/dump.txt | 164 +-
doc/dump_image.html | 142 +-
doc/dump_image.txt | 144 +-
doc/dump_modify.html | 686 +-
doc/dump_modify.txt | 679 +-
doc/dump_molfile.html | 137 +
doc/dump_molfile.txt | 126 +
doc/fix.html | 9 +-
doc/fix.txt | 10 +-
doc/fix_adapt.html | 39 +-
doc/fix_adapt.txt | 34 +-
doc/fix_addforce.html | 4 +-
doc/fix_addforce.txt | 4 +-
doc/fix_append_atoms.html | 18 +-
doc/fix_append_atoms.txt | 16 +-
doc/fix_atc.html | 331 +-
doc/fix_atc.txt | 352 +-
doc/fix_ave_atom.html | 9 +
doc/fix_ave_atom.txt | 9 +
doc/fix_ave_correlate.html | 7 +-
doc/fix_ave_correlate.txt | 7 +-
doc/fix_ave_histo.html | 7 +-
doc/fix_ave_histo.txt | 7 +-
doc/fix_ave_spatial.html | 14 +-
doc/fix_ave_spatial.txt | 11 +-
doc/fix_ave_time.html | 7 +-
doc/fix_ave_time.txt | 7 +-
doc/fix_bond_swap.html | 7 +
doc/fix_bond_swap.txt | 7 +
doc/fix_box_relax.html | 47 +-
doc/fix_box_relax.txt | 51 +-
doc/fix_colvars.html | 147 +
doc/fix_colvars.txt | 136 +
doc/fix_deform.html | 68 +-
doc/fix_deform.txt | 66 +-
doc/fix_deposit.html | 20 +-
doc/fix_deposit.txt | 20 +-
doc/fix_dt_reset.html | 23 +-
doc/fix_dt_reset.txt | 23 +-
doc/fix_efield.html | 140 +-
doc/fix_efield.txt | 139 +-
doc/fix_evaporate.html | 6 +-
doc/fix_evaporate.txt | 6 +-
doc/fix_external.html | 146 +-
doc/fix_external.txt | 140 +-
doc/fix_gcmc.html | 144 +-
doc/fix_gcmc.txt | 145 +-
doc/fix_gld.html | 171 +
doc/fix_gld.txt | 155 +
doc/fix_gravity.html | 2 +-
doc/fix_gravity.txt | 2 +-
doc/fix_heat.html | 63 +-
doc/fix_heat.txt | 63 +-
doc/fix_langevin.html | 88 +-
doc/fix_langevin.txt | 83 +-
doc/fix_lb_fluid.html | 388 +
doc/fix_lb_fluid.txt | 371 +
doc/fix_lb_momentum.html | 84 +
doc/fix_lb_momentum.txt | 73 +
doc/fix_lb_pc.html | 68 +
doc/fix_lb_pc.txt | 62 +
doc/fix_lb_rigid_pc_sphere.html | 158 +
doc/fix_lb_rigid_pc_sphere.txt | 146 +
doc/fix_lb_viscous.html | 100 +
doc/fix_lb_viscous.txt | 94 +
doc/fix_mesh_surface_stress_servo.html | 22 +-
doc/fix_mesh_surface_stress_servo.txt | 22 +-
doc/fix_move.html | 36 +-
doc/fix_move.txt | 36 +-
doc/fix_nh.html | 219 +-
doc/fix_nh.txt | 214 +-
doc/fix_nph_asphere.html | 24 +
doc/fix_nph_asphere.txt | 23 +
doc/fix_nph_sphere.html | 28 +-
doc/fix_nph_sphere.txt | 27 +-
doc/fix_nphug.html | 24 +
doc/fix_nphug.txt | 23 +
doc/fix_npt_asphere.html | 24 +
doc/fix_npt_asphere.txt | 23 +
doc/fix_npt_sphere.html | 28 +-
doc/fix_npt_sphere.txt | 27 +-
doc/fix_nve.html | 21 +-
doc/fix_nve.txt | 22 +-
doc/fix_nve_body.html | 67 +
doc/fix_nve_body.txt | 62 +
doc/fix_nve_limit.html | 9 +
doc/fix_nve_limit.txt | 9 +
doc/fix_nve_line.html | 4 +-
doc/fix_nve_line.txt | 4 +-
doc/fix_nve_sphere.html | 2 +-
doc/fix_nve_sphere.txt | 2 +-
doc/fix_nve_tri.html | 4 +-
doc/fix_nve_tri.txt | 4 +-
doc/fix_nvt_asphere.html | 24 +
doc/fix_nvt_asphere.txt | 23 +
doc/fix_nvt_sllod.html | 24 +
doc/fix_nvt_sllod.txt | 23 +
doc/fix_nvt_sphere.html | 30 +-
doc/fix_nvt_sphere.txt | 29 +-
doc/fix_orient_fcc.html | 4 +
doc/fix_orient_fcc.txt | 4 +
doc/fix_phonon.html | 221 +
doc/fix_phonon.txt | 202 +
doc/fix_qeq_comb.html | 7 +-
doc/fix_qeq_comb.txt | 7 +-
doc/fix_qeq_reax.html | 4 +-
doc/fix_qeq_reax.txt | 4 +-
doc/fix_reax_bonds.html | 36 +-
doc/fix_reax_bonds.txt | 36 +-
doc/fix_reaxc_species.html | 143 +
doc/fix_reaxc_species.txt | 132 +
doc/fix_recenter.html | 2 +-
doc/fix_recenter.txt | 2 +-
doc/fix_restrain.html | 129 +-
doc/fix_restrain.txt | 128 +-
doc/fix_rigid.html | 575 +-
doc/fix_rigid.txt | 574 +-
doc/fix_spring.html | 2 +-
doc/fix_spring.txt | 2 +-
doc/fix_spring_self.html | 2 +
doc/fix_spring_self.txt | 2 +
doc/fix_srd.html | 80 +-
doc/fix_srd.txt | 80 +-
doc/fix_store_state.html | 8 +-
doc/fix_store_state.txt | 8 +-
doc/fix_temp_berendsen.html | 32 +-
doc/fix_temp_berendsen.txt | 30 +-
doc/fix_temp_rescale.html | 38 +-
doc/fix_temp_rescale.txt | 34 +-
doc/fix_thermal_conductivity.html | 18 +-
doc/fix_thermal_conductivity.txt | 18 +-
doc/fix_ti_rs.html | 156 +
doc/fix_ti_rs.txt | 140 +
doc/fix_ti_spring.html | 175 +
doc/fix_ti_spring.txt | 160 +
doc/fix_ttm.html | 4 +
doc/fix_ttm.txt | 4 +
doc/fix_tune_kspace.html | 109 +
doc/fix_tune_kspace.txt | 102 +
doc/fix_viscosity.html | 18 +-
doc/fix_viscosity.txt | 18 +-
doc/fix_viscous.html | 13 +-
doc/fix_viscous.txt | 13 +-
doc/fix_wall.html | 97 +-
doc/fix_wall.txt | 95 +-
doc/fix_wall_gran.html | 74 +-
doc/fix_wall_gran.txt | 63 +-
doc/fix_wall_region.html | 6 +-
doc/fix_wall_region.txt | 6 +-
doc/gran_cohesion_sjkr.html | 56 +
doc/gran_cohesion_sjkr.txt | 50 +
doc/gran_cohesion_sjkr2.html | 57 +
doc/gran_cohesion_sjkr2.txt | 51 +
doc/gran_model_hertz.html | 114 +
doc/gran_model_hertz.txt | 96 +
doc/gran_model_hertz_stiffness.html | 116 +
doc/gran_model_hertz_stiffness.txt | 98 +
doc/gran_model_hooke.html | 154 +
doc/gran_model_hooke.txt | 135 +
doc/gran_model_hooke_stiffness.html | 135 +
doc/gran_model_hooke_stiffness.txt | 116 +
doc/gran_rolling_friction_cdt.html | 47 +
doc/gran_rolling_friction_cdt.txt | 41 +
doc/gran_rolling_friction_epsd.html | 72 +
doc/gran_rolling_friction_epsd.txt | 66 +
doc/gran_rolling_friction_epsd2.html | 50 +
doc/gran_rolling_friction_epsd2.txt | 44 +
doc/gran_tangential_history.html | 42 +
doc/gran_tangential_history.txt | 36 +
doc/gran_tangential_no_history.html | 38 +
doc/gran_tangential_no_history.txt | 32 +
doc/group.html | 87 +-
doc/group.txt | 89 +-
doc/group2ndx.html | 58 +
doc/group2ndx.txt | 51 +
doc/if.html | 7 +-
doc/if.txt | 7 +-
doc/improper_cossq.html | 94 +
doc/improper_cossq.txt | 88 +
doc/improper_fourier.html | 86 +
doc/improper_fourier.txt | 81 +
doc/improper_ring.html | 101 +
doc/improper_ring.txt | 95 +
doc/improper_style.html | 8 +-
doc/improper_style.txt | 8 +-
doc/kspace_modify.html | 204 +-
doc/kspace_modify.txt | 203 +-
doc/kspace_style.html | 283 +-
doc/kspace_style.txt | 265 +-
doc/lattice.html | 29 +-
doc/lattice.txt | 29 +-
doc/liggghts_3.X_tutorial.html | 111 +
doc/liggghts_3.X_tutorial.txt | 96 +
doc/log.html | 12 +-
doc/log.txt | 12 +-
doc/minimize.html | 5 +-
doc/minimize.txt | 5 +-
doc/neb.html | 289 +-
doc/neb.txt | 288 +-
doc/neigh_modify.html | 49 +-
doc/neigh_modify.txt | 49 +-
doc/next.html | 31 +-
doc/next.txt | 31 +-
doc/orient.html | 51 -
doc/orient.txt | 46 -
doc/origin.html | 46 -
doc/origin.txt | 44 -
doc/package.html | 48 +-
doc/package.txt | 48 +-
doc/pair_adp.html | 3 +
doc/pair_adp.txt | 3 +
doc/pair_airebo.html | 5 +
doc/pair_airebo.txt | 5 +
doc/pair_beck.html | 2 +
doc/pair_beck.txt | 1 +
doc/pair_body.html | 124 +
doc/pair_body.txt | 119 +
doc/pair_bop.html | 452 +
doc/pair_bop.txt | 408 +
doc/pair_born.html | 59 +-
doc/pair_born.txt | 54 +-
doc/pair_brownian.html | 18 +-
doc/pair_brownian.txt | 19 +-
doc/pair_buck.html | 53 +-
doc/pair_buck.txt | 51 +-
doc/pair_buck_coul.html | 178 -
doc/pair_buck_coul.txt | 166 -
doc/pair_buck_long.html | 179 +
doc/pair_buck_long.txt | 167 +
doc/pair_charmm.html | 34 +-
doc/pair_charmm.txt | 33 +-
doc/pair_class2.html | 5 +-
doc/pair_class2.txt | 4 +-
doc/pair_coeff.html | 61 +-
doc/pair_coeff.txt | 61 +-
doc/pair_colloid.html | 2 +
doc/pair_colloid.txt | 1 +
doc/pair_comb.html | 215 +-
doc/pair_comb.txt | 214 +-
doc/pair_coul.html | 113 +-
doc/pair_coul.txt | 99 +-
doc/pair_dipole.html | 123 +-
doc/pair_dipole.txt | 116 +-
doc/pair_dpd.html | 16 +-
doc/pair_dpd.txt | 16 +-
doc/pair_dsmc.html | 12 +-
doc/pair_dsmc.txt | 12 +-
doc/pair_eam.html | 37 +-
doc/pair_eam.txt | 38 +-
doc/pair_edip.html | 3 +
doc/pair_edip.txt | 3 +
doc/pair_eff.html | 147 +-
doc/pair_eff.txt | 145 +-
doc/pair_eim.html | 3 +
doc/pair_eim.txt | 3 +
doc/pair_gauss.html | 34 +-
doc/pair_gauss.txt | 32 +-
doc/pair_gayberne.html | 8 +-
doc/pair_gayberne.txt | 8 +-
doc/pair_gran.html | 279 +-
doc/pair_gran.txt | 267 +-
doc/pair_gromacs.html | 12 +-
doc/pair_gromacs.txt | 12 +-
doc/pair_hbond_dreiding.html | 45 +-
doc/pair_hbond_dreiding.txt | 45 +-
doc/pair_hybrid.html | 22 +
doc/pair_hybrid.txt | 22 +
doc/pair_kim.html | 235 +-
doc/pair_kim.txt | 238 +-
doc/pair_lcbop.html | 103 +
doc/pair_lcbop.txt | 97 +
doc/pair_list.html | 154 +
doc/pair_list.txt | 144 +
doc/pair_lj.html | 196 +-
doc/pair_lj.txt | 186 +-
doc/pair_lj_coul.html | 181 -
doc/pair_lj_coul.txt | 169 -
doc/pair_lj_long.html | 234 +
doc/pair_lj_long.txt | 224 +
doc/pair_lj_smooth_linear.html | 2 +-
doc/pair_lj_smooth_linear.txt | 2 +-
doc/pair_lubricate.html | 79 +-
doc/pair_lubricate.txt | 79 +-
doc/pair_lubricateU.html | 76 +-
doc/pair_lubricateU.txt | 78 +-
doc/pair_meam.html | 3 +
doc/pair_meam.txt | 3 +
doc/pair_meam_spline.html | 3 +
doc/pair_meam_spline.txt | 3 +
doc/pair_meam_sw_spline.html | 146 +
doc/pair_meam_sw_spline.txt | 139 +
doc/pair_mie.html | 107 +
doc/pair_mie.txt | 101 +
doc/pair_modify.html | 31 +-
doc/pair_modify.txt | 31 +-
doc/pair_nb3b_harmonic.html | 128 +
doc/pair_nb3b_harmonic.txt | 122 +
doc/pair_nm.html | 182 +
doc/pair_nm.txt | 168 +
doc/pair_peri.html | 50 +-
doc/pair_peri.txt | 48 +-
doc/pair_reax_c.html | 69 +-
doc/pair_reax_c.txt | 69 +-
doc/pair_resquared.html | 2 +-
doc/pair_resquared.txt | 2 +-
doc/pair_soft.html | 2 +
doc/pair_soft.txt | 1 +
doc/pair_sph_taitwater_morris.html | 2 +-
doc/pair_sph_taitwater_morris.txt | 2 +-
doc/pair_style.html | 26 +-
doc/pair_style.txt | 26 +-
doc/pair_sw.html | 7 +
doc/pair_sw.txt | 6 +
doc/pair_table.html | 19 +-
doc/pair_table.txt | 19 +-
doc/pair_tersoff.html | 3 +
doc/pair_tersoff.txt | 3 +
doc/pair_tersoff_mod.html | 201 +
doc/pair_tersoff_mod.txt | 190 +
doc/pair_tersoff_zbl.html | 5 +-
doc/pair_tersoff_zbl.txt | 5 +-
doc/pair_yukawa_colloid.html | 16 +-
doc/pair_yukawa_colloid.txt | 14 +-
doc/pair_zbl.html | 136 +
doc/pair_zbl.txt | 129 +
doc/print.html | 40 +-
doc/print.txt | 37 +-
doc/read_data.html | 227 +-
doc/read_data.txt | 197 +-
doc/read_dump.html | 337 +
doc/read_dump.txt | 325 +
doc/read_restart.html | 73 +-
doc/read_restart.txt | 73 +-
doc/region.html | 17 +
doc/region.txt | 17 +
doc/replicate.html | 32 +-
doc/replicate.txt | 32 +-
doc/rerun.html | 206 +
doc/rerun.txt | 198 +
doc/reset_timestep.html | 54 +-
doc/reset_timestep.txt | 62 +-
doc/restart.html | 127 +-
doc/restart.txt | 124 +-
doc/run_style.html | 24 +-
doc/run_style.txt | 24 +-
doc/set.html | 94 +-
doc/set.txt | 94 +-
doc/shell.html | 11 +-
doc/shell.txt | 11 +-
doc/tad.html | 2 +-
doc/tad.txt | 2 +-
doc/thermo.html | 23 +-
doc/thermo.txt | 23 +-
doc/thermo_modify.html | 38 +-
doc/thermo_modify.txt | 35 +-
doc/thermo_style.html | 41 +-
doc/thermo_style.txt | 41 +-
doc/units.html | 55 +-
doc/units.txt | 57 +-
doc/variable.html | 284 +-
doc/variable.txt | 284 +-
doc/velocity.html | 20 +-
doc/velocity.txt | 20 +-
doc/write_data.html | 125 +
doc/write_data.txt | 117 +
doc/write_dump.html | 101 +
doc/write_dump.txt | 91 +
doc/write_restart.html | 70 +-
doc/write_restart.txt | 68 +-
examples/LAMMPS/ASPHERE/README | 36 +
examples/LAMMPS/ASPHERE/box/box.py | 10 +
examples/LAMMPS/ASPHERE/box/data.box | 852 +
examples/LAMMPS/ASPHERE/box/in.box | 107 +
examples/LAMMPS/ASPHERE/box/in.box.mp | 108 +
examples/LAMMPS/ASPHERE/box/log.box.10Sep13 | 289 +
examples/LAMMPS/ASPHERE/box/log.box.mp.10Sep13 | 290 +
examples/LAMMPS/ASPHERE/dimer/data.dimer | 412 +
examples/LAMMPS/ASPHERE/dimer/dimer.py | 10 +
examples/LAMMPS/ASPHERE/dimer/in.dimer | 104 +
examples/LAMMPS/ASPHERE/dimer/in.dimer.mp | 105 +
examples/LAMMPS/ASPHERE/dimer/log.dimer.10Sep13 | 285 +
examples/LAMMPS/ASPHERE/dimer/log.dimer.mp.10Sep13 | 236 +
examples/LAMMPS/ASPHERE/ellipsoid/in.ellipsoid | 116 +
examples/LAMMPS/ASPHERE/ellipsoid/in.ellipsoid.mp | 117 +
.../LAMMPS/ASPHERE/ellipsoid/log.ellipsoid.10Sep13 | 296 +
.../ASPHERE/ellipsoid/log.ellipsoid.mp.10Sep13 | 247 +
examples/LAMMPS/ASPHERE/line/data.line | 713 +
examples/LAMMPS/ASPHERE/line/data.line.srd | 813 +
examples/LAMMPS/ASPHERE/line/in.line | 53 +
examples/LAMMPS/ASPHERE/line/in.line.srd | 105 +
examples/LAMMPS/ASPHERE/line/line.py | 14 +
examples/LAMMPS/ASPHERE/line/line.srd.py | 14 +
examples/LAMMPS/ASPHERE/line/line.srd.viz.py | 16 +
examples/LAMMPS/ASPHERE/line/line.viz.py | 13 +
examples/LAMMPS/ASPHERE/line/log.line.10Sep13 | 212 +
examples/LAMMPS/ASPHERE/line/log.line.srd.10Sep13 | 243 +
examples/LAMMPS/ASPHERE/poly/in.poly | 113 +
examples/LAMMPS/ASPHERE/poly/in.poly.mp | 114 +
examples/LAMMPS/ASPHERE/poly/log.poly.10Sep13 | 288 +
examples/LAMMPS/ASPHERE/poly/log.poly.mp.10Sep13 | 239 +
examples/LAMMPS/ASPHERE/star/data.star | 552 +
examples/LAMMPS/ASPHERE/star/in.star | 107 +
examples/LAMMPS/ASPHERE/star/in.star.mp | 108 +
examples/LAMMPS/ASPHERE/star/log.star.10Sep13 | 289 +
examples/LAMMPS/ASPHERE/star/log.star.mp.10Sep13 | 290 +
examples/LAMMPS/ASPHERE/star/star.py | 11 +
examples/LAMMPS/ASPHERE/tri/data.tri.srd | 3013 +
examples/LAMMPS/ASPHERE/tri/in.tri.srd | 105 +
examples/LAMMPS/ASPHERE/tri/log.tri.srd.10Sep13 | 242 +
examples/LAMMPS/ASPHERE/tri/tri.srd.py | 14 +
examples/LAMMPS/ASPHERE/tri/tri.srd.viz.py | 18 +
examples/LAMMPS/COUPLE/README | 40 +
examples/LAMMPS/COUPLE/fortran/README | 8 +
examples/LAMMPS/COUPLE/fortran/libfwrapper.c | 136 +
examples/LAMMPS/COUPLE/fortran2/LAMMPS-wrapper.cpp | 236 +
examples/LAMMPS/COUPLE/fortran2/LAMMPS-wrapper.h | 41 +
examples/LAMMPS/COUPLE/fortran2/LAMMPS.F90 | 942 +
examples/LAMMPS/COUPLE/fortran2/README | 265 +
examples/LAMMPS/COUPLE/fortran2/in.simple | 16 +
examples/LAMMPS/COUPLE/fortran2/makefile | 36 +
examples/LAMMPS/COUPLE/fortran2/simple.f90 | 111 +
examples/LAMMPS/COUPLE/lammps_quest/Makefile.g++ | 47 +
examples/LAMMPS/COUPLE/lammps_quest/README | 64 +
examples/LAMMPS/COUPLE/lammps_quest/in.lammps | 20 +
.../LAMMPS/COUPLE}/lammps_quest/lmppath.h | 0
examples/LAMMPS/COUPLE/lammps_quest/lmpqst.cpp | 264 +
.../LAMMPS/COUPLE}/lammps_quest/log.lammps.1 | 0
.../LAMMPS/COUPLE}/lammps_quest/log.lammps.4 | 0
.../LAMMPS/COUPLE}/lammps_quest/qstexe.h | 0
.../LAMMPS/COUPLE}/lammps_quest/si_111.in | 0
.../LAMMPS/COUPLE}/lammps_spparks/Makefile.g++ | 0
examples/LAMMPS/COUPLE/lammps_spparks/README | 74 +
examples/LAMMPS/COUPLE/lammps_spparks/in.lammps | 114 +
.../LAMMPS/COUPLE}/lammps_spparks/in.spparks | 0
.../LAMMPS/COUPLE}/lammps_spparks/lmppath.h | 0
.../LAMMPS/COUPLE}/lammps_spparks/lmpspk.cpp | 0
.../LAMMPS/COUPLE}/lammps_spparks/log.lammps.1 | 0
.../LAMMPS/COUPLE}/lammps_spparks/log.lammps.4 | 0
.../LAMMPS/COUPLE}/lammps_spparks/log.spparks.1 | 0
.../LAMMPS/COUPLE}/lammps_spparks/log.spparks.4 | 0
.../LAMMPS/COUPLE}/lammps_spparks/spkpath.h | 0
.../LAMMPS/COUPLE}/library/Makefile.g++ | 0
{couple => examples/LAMMPS/COUPLE}/library/README | 0
.../LAMMPS/COUPLE}/library/error.cpp | 0
{couple => examples/LAMMPS/COUPLE}/library/error.h | 0
.../LAMMPS/COUPLE}/library/files.cpp | 0
{couple => examples/LAMMPS/COUPLE}/library/files.h | 0
.../LAMMPS/COUPLE}/library/irregular.cpp | 0
.../LAMMPS/COUPLE}/library/irregular.h | 0
.../LAMMPS/COUPLE}/library/lammps_data_write.cpp | 0
.../LAMMPS/COUPLE}/library/lammps_data_write.h | 0
.../LAMMPS/COUPLE}/library/many2many.cpp | 0
.../LAMMPS/COUPLE}/library/many2many.h | 0
.../LAMMPS/COUPLE}/library/many2one.cpp | 0
.../LAMMPS/COUPLE}/library/many2one.h | 0
.../LAMMPS/COUPLE}/library/memory.cpp | 0
.../LAMMPS/COUPLE}/library/memory.h | 0
.../LAMMPS/COUPLE}/library/one2many.cpp | 0
.../LAMMPS/COUPLE}/library/one2many.h | 0
.../LAMMPS/COUPLE}/library/send2one.cpp | 0
.../LAMMPS/COUPLE}/library/send2one.h | 0
examples/LAMMPS/COUPLE/simple/README | 86 +
examples/LAMMPS/COUPLE/simple/in.lj | 26 +
.../LAMMPS/COUPLE}/simple/log.simple.c++.1 | 0
.../LAMMPS/COUPLE}/simple/log.simple.c++.4 | 0
examples/LAMMPS/COUPLE/simple/simple.c | 116 +
examples/LAMMPS/COUPLE/simple/simple.cpp | 122 +
examples/LAMMPS/COUPLE/simple/simple.f90 | 135 +
examples/LAMMPS/ELASTIC/displace.mod | 24 +-
examples/LAMMPS/ELASTIC/displace_restart.mod | 134 +
examples/LAMMPS/ELASTIC/displace_reverse.mod | 162 +
examples/LAMMPS/ELASTIC/in.elastic | 2 +-
examples/LAMMPS/KAPPA/README | 89 +
examples/LAMMPS/KAPPA/in.heat | 76 +
examples/LAMMPS/KAPPA/in.heatflux | 79 +
examples/LAMMPS/KAPPA/in.langevin | 88 +
examples/LAMMPS/KAPPA/in.mp | 71 +
examples/LAMMPS/KAPPA/log.heat.12Sep13 | 195 +
examples/LAMMPS/KAPPA/log.heatflux.12Sep13 | 208 +
examples/LAMMPS/KAPPA/log.langevin.12Sep13 | 215 +
examples/LAMMPS/KAPPA/log.mp.12Sep13 | 200 +
examples/LAMMPS/KAPPA/profile.heat.12Sep13 | 423 +
examples/LAMMPS/KAPPA/profile.heatflux.12Sep13 | 10254 ++
examples/LAMMPS/KAPPA/profile.langevin.12Sep13 | 423 +
examples/LAMMPS/KAPPA/profile.mp.12Sep13 | 843 +
examples/LAMMPS/README | 74 +-
examples/LAMMPS/USER/atc/README | 255 +-
.../LAMMPS/USER/atc/bar1d_thermal/Ar_thermal.mat | 11 -
examples/LAMMPS/USER/atc/bar1d_thermal/bar1d.log | 286 -
.../LAMMPS/USER/atc/bar1d_thermal/bar1d_flux.log | 334 -
examples/LAMMPS/USER/atc/bar1d_thermal/in.bar1d | 100 -
.../LAMMPS/USER/atc/bar1d_thermal/in.bar1d_flux | 103 -
.../USER/atc/bar1d_thermal/in.bar1d_frac_step | 112 -
examples/LAMMPS/USER/atc/bar1d_thermal/temp.init | 2903 -
.../USER/atc/bar1d_two_temperature/Ar_ttm.mat | 35 -
.../USER/atc/bar1d_two_temperature/Cu_ttm.mat | 17 -
.../USER/atc/bar1d_two_temperature/bar1d_ttm.log | 537 -
.../atc/bar1d_two_temperature/gaussianIC_ttm.log | 168 -
.../USER/atc/bar1d_two_temperature/in.bar1d_ttm | 105 -
.../atc/bar1d_two_temperature/in.gaussianIC_ttm | 97 -
.../USER/atc/bar1d_two_temperature/in.no_atoms | 57 -
.../atc/bar1d_two_temperature/in.uniform_exchange | 67 -
.../atc/bar1d_two_temperature/in.uniform_heating | 74 -
.../USER/atc/bar1d_two_temperature/no_atoms.log | 190 -
.../USER/atc/bar1d_two_temperature/temp.init | 6935 --
.../atc/bar1d_two_temperature/uniform_exchange.log | 672 -
.../uniform_exchange_init.data | 6935 --
.../atc/bar1d_two_temperature/uniform_heating.log | 91 -
.../uniform_heating_init.data | 4631 -
.../LAMMPS/USER/atc/cauchy_born/Ar_CauchyBorn.mat | 7 +
.../USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat | 7 +
.../LAMMPS/USER/atc/cauchy_born/Au_CauchyBorn.mat | 6 +
.../USER/atc/cauchy_born/Au_CauchyBorn_linear.mat | 6 +
examples/LAMMPS/USER/atc/cauchy_born/Au_eam.mat | 5 +
.../LAMMPS/USER/atc/cauchy_born/Au_eam_linear.mat | 6 +
.../LAMMPS/USER/atc/cauchy_born/Cu_CauchyBorn.mat | 5 +
.../LAMMPS/USER/atc/cauchy_born/cb_biaxial.screen | 402 +
.../LAMMPS/USER/atc/cauchy_born/cb_shear.screen | 386 +
.../USER/atc/cauchy_born/cb_unistrain.screen | 124 +
.../USER/atc/cauchy_born/cb_unistrain_eam.screen | 146 +
.../atc/cauchy_born/cb_unistrain_eam_linear.screen | 160 +
.../atc/cauchy_born/cb_unistrain_linear.screen | 163 +
.../USER/atc/cauchy_born/cb_volumetric.screen | 391 +
.../LAMMPS/USER/atc/cauchy_born/flying_cube.screen | 569 +
.../LAMMPS/USER/atc/cauchy_born/ftcb_constV.screen | 302 +
examples/LAMMPS/USER/atc/cauchy_born/in.cb_biaxial | 54 +
examples/LAMMPS/USER/atc/cauchy_born/in.cb_shear | 55 +
.../LAMMPS/USER/atc/cauchy_born/in.cb_unistrain | 46 +
.../USER/atc/cauchy_born/in.cb_unistrain_eam | 51 +
.../atc/cauchy_born/in.cb_unistrain_eam_linear | 51 +
.../USER/atc/cauchy_born/in.cb_unistrain_linear | 54 +
.../LAMMPS/USER/atc/cauchy_born/in.cb_volumetric | 49 +
.../LAMMPS/USER/atc/cauchy_born/in.flying_cube | 61 +
.../LAMMPS/USER/atc/cauchy_born/in.ftcb_constV | 74 +
examples/LAMMPS/USER/atc/cauchy_born/in.read_xref | 37 +
.../LAMMPS/USER/atc/cauchy_born/read_xref.screen | 84 +
.../LAMMPS/USER/atc/drift_diffusion/Ar_ddm.mat | 37 +
.../LAMMPS/USER/atc/drift_diffusion/CNT_ddm.mat | 41 +
.../LAMMPS/USER/atc/drift_diffusion/Cu_cddm.mat | 45 +
.../atc/drift_diffusion/SiGe_ddm_schrodinger.mat | 86 +
.../drift_diffusion/SiVacuum_cddm_schrodinger.mat | 64 +
.../drift_diffusion/SiVacuum_ddm_schrodinger.mat | 52 +
.../LAMMPS/USER/atc/drift_diffusion/Si_ddm.mat | 35 +
.../LAMMPS/USER/atc/drift_diffusion/Si_ddm_eq.mat | 44 +
.../atc/drift_diffusion/Si_ddm_schrodinger.mat | 41 +
.../atc/drift_diffusion/Si_ddm_thermopower.mat | 36 +
.../atc/drift_diffusion/convective_pulse.screen | 145 +
.../atc/drift_diffusion/ddm_schrodinger.screen | 79 +
.../USER/atc/drift_diffusion/finite_well.screen | 106 +
.../USER/atc/drift_diffusion/in.convective_pulse | 72 +
.../USER/atc/drift_diffusion/in.ddm_schrodinger | 66 +
.../LAMMPS/USER/atc/drift_diffusion/in.finite_well | 75 +
.../USER/atc/drift_diffusion/in.no_atoms_ddm | 65 +
.../USER/atc/drift_diffusion/in.null_material_ddm | 79 +
.../USER/atc/drift_diffusion/in.poisson1d_noatoms | 41 +
.../USER/atc/drift_diffusion/in.poisson2d_noatoms | 73 +
.../in.schrodinger-poisson2d_Jconstraint | 138 +
.../in.schrodinger-poisson2d_convective | 150 +
.../in.schrodinger-poisson2d_noatoms | 124 +
.../USER/atc/drift_diffusion/no_atoms_ddm.screen | 143 +
.../atc/drift_diffusion/null_material_ddm.screen | 159 +
.../atc/drift_diffusion/poisson1d_noatoms.screen | 42 +
.../atc/drift_diffusion/poisson2d_noatoms.screen | 110 +
.../schrodinger-poisson2d_Jconstraint.screen | 163 +
.../schrodinger-poisson2d_convective.screen | 220 +
.../schrodinger-poisson2d_noatoms.screen | 192 +
examples/LAMMPS/USER/atc/elastic/Ar_CauchyBorn.mat | 8 +
.../USER/atc/elastic/Ar_CauchyBornLinear.mat | 9 +
examples/LAMMPS/USER/atc/elastic/Ar_damped.mat | 37 +
examples/LAMMPS/USER/atc/elastic/Ar_elastic.mat | 29 +
.../LAMMPS/USER/atc/elastic/Ar_thermo_elastic.mat | 11 +
examples/LAMMPS/USER/atc/elastic/Au_elastic.mat | 18 +
examples/LAMMPS/USER/atc/elastic/CNT.mat | 1315 +
.../LAMMPS/USER/atc/elastic/CNT_electrostatic.mat | 18 +
.../LAMMPS/USER/atc/elastic/CNT_electrostatic2.mat | 21 +
examples/LAMMPS/USER/atc/elastic/CNT_id.mat | 11 +
examples/LAMMPS/USER/atc/elastic/bar1d.screen | 270 +
.../LAMMPS/USER/atc/elastic/bar1d_damped.screen | 385 +
examples/LAMMPS/USER/atc/elastic/bar1d_flux.screen | 281 +
.../LAMMPS/USER/atc/elastic/bar1d_frac_step.screen | 228 +
.../USER/atc/elastic/bar1d_ghost_flux.screen | 211 +
.../USER/atc/elastic/bar1d_thermo_elastic.screen | 113 +
.../USER/atc/elastic/cnt_electrostatic.screen | 1213 +
.../USER/atc/elastic/cnt_electrostatic2.screen | 215 +
.../USER/atc/elastic/cnt_fixed_charge.screen | 351 +
examples/LAMMPS/USER/atc/elastic/eam_energy.screen | 335 +
.../USER/atc/elastic/electron_density.screen | 267 +
.../USER/atc/elastic/electrostatic_bending.screen | 846 +
.../atc/elastic/electrostatic_bending_dos.screen | 633 +
examples/LAMMPS/USER/atc/elastic/in.bar1d | 91 +
examples/LAMMPS/USER/atc/elastic/in.bar1d_damped | 116 +
examples/LAMMPS/USER/atc/elastic/in.bar1d_flux | 98 +
.../LAMMPS/USER/atc/elastic/in.bar1d_frac_step | 99 +
.../LAMMPS/USER/atc/elastic/in.bar1d_ghost_flux | 101 +
.../USER/atc/elastic/in.bar1d_thermo_elastic | 139 +
.../LAMMPS/USER/atc/elastic/in.cnt_electrostatic | 107 +
.../LAMMPS/USER/atc/elastic/in.cnt_electrostatic2 | 118 +
.../LAMMPS/USER/atc/elastic/in.cnt_fixed_charge | 145 +
examples/LAMMPS/USER/atc/elastic/in.eam_energy | 80 +
.../LAMMPS/USER/atc/elastic/in.electron_density | 74 +
.../USER/atc/elastic/in.electrostatic_bending | 186 +
.../USER/atc/elastic/in.electrostatic_bending_dos | 164 +
examples/LAMMPS/USER/atc/elastic/in.no_atoms | 42 +
examples/LAMMPS/USER/atc/elastic/in.no_atoms_cb | 43 +
.../LAMMPS/USER/atc/elastic/in.no_atoms_cb_linear | 42 +
examples/LAMMPS/USER/atc/elastic/no_atoms.screen | 75 +
.../LAMMPS/USER/atc/elastic/no_atoms_cb.screen | 78 +
.../USER/atc/elastic/no_atoms_cb_linear.screen | 79 +
examples/LAMMPS/USER/atc/fluids/Ar_elastic.mat | 8 +
.../LAMMPS/USER/atc/fluids/Ar_electrostatic.mat | 8 +
examples/LAMMPS/USER/atc/fluids/Ar_liquid.mat | 8 +
examples/LAMMPS/USER/atc/fluids/Ar_species.mat | 5 +
examples/LAMMPS/USER/atc/fluids/Ar_species_dl.mat | 8 +
examples/LAMMPS/USER/atc/fluids/Ar_thermal.mat | 9 +
.../LAMMPS/USER/atc/fluids/Ar_visc_no_atoms.mat | 6 +
examples/LAMMPS/USER/atc/fluids/Ar_viscosity.mat | 9 +
.../LAMMPS/USER/atc/fluids/bar1d_fluids.screen | 263 +
.../LAMMPS/USER/atc/fluids/concentration.screen | 169 +
.../USER/atc/fluids/conducting_interface.screen | 184 +
examples/LAMMPS/USER/atc/fluids/dielectric.mat | 15 +
.../USER/atc/fluids/dielectric_interface.screen | 184 +
.../LAMMPS/USER/atc/fluids/double_layer.screen | 203 +
examples/LAMMPS/USER/atc/fluids/in.bar1d_fluids | 98 +
examples/LAMMPS/USER/atc/fluids/in.concentration | 172 +
.../LAMMPS/USER/atc/fluids/in.conducting_interface | 111 +
.../LAMMPS/USER/atc/fluids/in.dielectric_interface | 106 +
examples/LAMMPS/USER/atc/fluids/in.double_layer | 100 +
.../LAMMPS/USER/atc/fluids/in.liquid_electrostatic | 63 +
examples/LAMMPS/USER/atc/fluids/in.opp_force | 70 +
examples/LAMMPS/USER/atc/fluids/in.poisson | 69 +
examples/LAMMPS/USER/atc/fluids/in.shear_flow | 84 +
examples/LAMMPS/USER/atc/fluids/in.shear_no_atoms | 32 +
.../USER/atc/fluids/liquid_electrostatic.screen | 143 +
examples/LAMMPS/USER/atc/fluids/opp_force.screen | 146 +
examples/LAMMPS/USER/atc/fluids/poisson.screen | 260 +
examples/LAMMPS/USER/atc/fluids/shear_flow.screen | 65 +
.../LAMMPS/USER/atc/fluids/shear_no_atoms.screen | 91 +
examples/LAMMPS/USER/atc/hardy/consistency.screen | 898 +-
.../USER/atc/hardy/eam_kernel_convergence.screen | 3334 +-
.../USER/atc/hardy/eam_unistrain_cell.screen | 83 +-
.../USER/atc/hardy/eam_unistrain_mesh.screen | 122 +-
.../USER/atc/hardy/eam_unistrain_qcylinder.screen | 80 +-
.../USER/atc/hardy/eam_unistrain_qsphere.screen | 80 +-
.../USER/atc/hardy/eam_unistrain_step.screen | 122 +-
.../USER/atc/hardy/eam_volume_stretch.screen | 143 +-
.../LAMMPS/USER/atc/hardy/eshelby_static.screen | 1273 +
examples/LAMMPS/USER/atc/hardy/in.consistency | 37 +-
.../USER/atc/hardy/in.eam_kernel_convergence | 35 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_cell | 43 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_mesh | 45 +-
.../USER/atc/hardy/in.eam_unistrain_qcylinder | 44 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_qsphere | 45 +-
.../LAMMPS/USER/atc/hardy/in.eam_unistrain_step | 45 +-
.../LAMMPS/USER/atc/hardy/in.eam_volume_stretch | 46 +-
examples/LAMMPS/USER/atc/hardy/in.eshelby_static | 132 +
examples/LAMMPS/USER/atc/hardy/in.nvt | 44 +-
examples/LAMMPS/USER/atc/hardy/nvt.data | 1020 +
examples/LAMMPS/USER/atc/hardy/nvt.screen | 92 +
examples/LAMMPS/USER/atc/mesh/Ar_ttm.mat | 35 +
examples/LAMMPS/USER/atc/mesh/Si.mat | 9 +
.../LAMMPS/USER/atc/mesh/gaussianIC1d_hex.screen | 108 +
.../LAMMPS/USER/atc/mesh/gaussianIC2d_hex.screen | 287 +
.../atc/mesh/gaussianIC2d_hex20_uniform.screen | 107 +
.../atc/mesh/gaussianIC2d_hex27_uniform.screen | 99 +
.../USER/atc/mesh/gaussianIC2d_hex_uniform.screen | 126 +
.../LAMMPS/USER/atc/mesh/gaussianIC2d_tet.screen | 102 +
examples/LAMMPS/USER/atc/mesh/in.gaussianIC1d_hex | 56 +
examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_hex | 69 +
.../USER/atc/mesh/in.gaussianIC2d_hex20_uniform | 37 +
.../USER/atc/mesh/in.gaussianIC2d_hex27_uniform | 37 +
examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_tet | 40 +
examples/LAMMPS/USER/atc/mesh/in.kernel2d_hex | 32 +
examples/LAMMPS/USER/atc/mesh/in.kernel2d_tet | 28 +
examples/LAMMPS/USER/atc/mesh/in.mesh2d_tet | 29 +
examples/LAMMPS/USER/atc/mesh/in.semicircle | 101 +
examples/LAMMPS/USER/atc/mesh/kernel2d_hex.screen | 81 +
examples/LAMMPS/USER/atc/mesh/kernel2d_tet.screen | 77 +
examples/LAMMPS/USER/atc/mesh/mesh2d_tet.screen | 78 +
examples/LAMMPS/USER/atc/mesh/semicircle.screen | 205 +
.../LAMMPS/USER/atc/molecule/harmonic_bonds.screen | 123 +
.../LAMMPS/USER/atc/molecule/in.harmonic_bonds | 55 +
examples/LAMMPS/USER/atc/molecule/in.polarize | 120 +
examples/LAMMPS/USER/atc/molecule/in.quartic_bonds | 60 +
examples/LAMMPS/USER/atc/molecule/in.water | 96 +
examples/LAMMPS/USER/atc/molecule/polarize.screen | 316 +
.../LAMMPS/USER/atc/molecule/quartic_bonds.screen | 116 +
examples/LAMMPS/USER/atc/molecule/water.mat | 5 +
examples/LAMMPS/USER/atc/molecule/water.screen | 100 +
examples/LAMMPS/USER/atc/thermal/Ar_thermal.mat | 14 +
examples/LAMMPS/USER/atc/thermal/bar1d.screen | 374 +
.../LAMMPS/USER/atc/thermal/bar1d_all_atoms.screen | 103 +
.../LAMMPS/USER/atc/thermal/bar1d_combined.screen | 165 +
examples/LAMMPS/USER/atc/thermal/bar1d_flux.screen | 252 +
.../LAMMPS/USER/atc/thermal/bar1d_frac_step.screen | 177 +
.../LAMMPS/USER/atc/thermal/bar1d_hoover.screen | 130 +
.../USER/atc/thermal/bar1d_interpolate.screen | 207 +
.../LAMMPS/USER/atc/thermal/bar1d_lumped.screen | 295 +
examples/LAMMPS/USER/atc/thermal/in.bar1d | 79 +
.../LAMMPS/USER/atc/thermal/in.bar1d_all_atoms | 101 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_combined | 87 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_flux | 79 +
.../LAMMPS/USER/atc/thermal/in.bar1d_frac_step | 80 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_hoover | 138 +
.../LAMMPS/USER/atc/thermal/in.bar1d_interpolate | 80 +
examples/LAMMPS/USER/atc/thermal/in.bar1d_lumped | 85 +
examples/LAMMPS/USER/atc/thermal/in.no_atoms | 56 +
examples/LAMMPS/USER/atc/thermal/no_atoms.screen | 351 +
.../LAMMPS/USER/atc/two_temperature/Ar_ttm.mat | 35 +
.../LAMMPS/USER/atc/two_temperature/Cu_ttm.mat | 17 +
.../USER/atc/two_temperature/bar1d_ttm.screen | 447 +
.../LAMMPS/USER/atc/two_temperature/cutout.screen | 279 +
.../USER/atc/two_temperature/gaussianIC_ttm.screen | 169 +
.../LAMMPS/USER/atc/two_temperature/in.bar1d_ttm | 86 +
examples/LAMMPS/USER/atc/two_temperature/in.cutout | 87 +
.../USER/atc/two_temperature/in.gaussianIC_ttm | 94 +
.../LAMMPS/USER/atc/two_temperature/in.no_atoms | 61 +
.../LAMMPS/USER/atc/two_temperature/in.restart | 117 +
.../USER/atc/two_temperature/in.uniform_exchange | 66 +
.../USER/atc/two_temperature/in.uniform_heating | 53 +
.../USER/atc/two_temperature/no_atoms.screen | 203 +
.../LAMMPS/USER/atc/two_temperature/restart.screen | 160 +
.../atc/two_temperature/uniform_exchange.screen | 618 +
.../atc/two_temperature/uniform_heating.screen | 134 +
.../LAMMPS/{peptide => USER/colvars}/data.peptide | 0
examples/LAMMPS/USER/colvars/in.peptide-colvars | 48 +
examples/LAMMPS/USER/colvars/in.peptide-colvars2 | 40 +
examples/LAMMPS/USER/colvars/log.peptide-colvars-1 | 516 +
examples/LAMMPS/USER/colvars/log.peptide-colvars-4 | 516 +
.../LAMMPS/USER/colvars/log.peptide-colvars2-1 | 182 +
.../LAMMPS/USER/colvars/log.peptide-colvars2-4 | 182 +
examples/LAMMPS/USER/colvars/out.colvars.state | 22 +
examples/LAMMPS/USER/colvars/out.colvars.traj | 102 +
examples/LAMMPS/USER/colvars/out2.colvars.state | 22 +
examples/LAMMPS/USER/colvars/out2.colvars.traj | 102 +
examples/LAMMPS/USER/colvars/peptide.colvars | 39 +
examples/LAMMPS/USER/colvars/peptide.colvars2 | 26 +
examples/LAMMPS/USER/colvars/peptide.psf | 126 +
.../LAMMPS/USER/colvars/peptide2.colvars.state | 17 +
examples/LAMMPS/USER/colvars/peptide2.colvars.traj | 102 +
.../eff/Auger-Adamantane/in.adamantane_ionized.nve | 2 +-
examples/LAMMPS/USER/eff/Be-solid/in.Be-solid.spe | 2 +-
examples/LAMMPS/USER/eff/ECP/Si2H6/data.Si2H6 | 2 +-
examples/LAMMPS/USER/eff/ECP/Si2H6/in.Si2H6 | 2 +-
examples/LAMMPS/USER/eff/ECP/SiC/bulk/data.SiC | 5018 +
examples/LAMMPS/USER/eff/ECP/SiC/bulk/in.SiC | 41 +
examples/LAMMPS/USER/eff/ECP/SiH4/data.SiH4 | 2 +-
examples/LAMMPS/USER/eff/ECP/SiH4/in.SiH4 | 2 +-
examples/LAMMPS/USER/eff/ECP/SiH4/in.SiH4.ang | 2 +-
examples/LAMMPS/USER/eff/H/in.h_atom.spe.ang | 2 +-
examples/LAMMPS/USER/eff/H/in.h_atom.spe.bohr | 2 +-
examples/LAMMPS/USER/eff/H2/in.h2 | 2 +-
examples/LAMMPS/USER/eff/H_plasma/in.h2bulk.npt | 2 +-
examples/LAMMPS/USER/eff/H_plasma/in.h2bulk.nve | 2 +-
.../LAMMPS/USER/eff/H_plasma/in.h2bulk.nve.ang | 2 +-
.../USER/eff/Li-dendritic/in.Li-dendritic.min | 2 +-
.../USER/eff/Li-dendritic/in.Li-dendritic.nvt | 2 +-
examples/LAMMPS/USER/eff/Li-solid/in.Li.ang | 6 +-
examples/LAMMPS/USER/eff/Li-solid/in.Li.bohr | 2 +-
.../LAMMPS/USER/eff/fixed-core/CH4/in.CH4fc.ang | 2 +-
.../LAMMPS/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 2 +-
.../USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 2 +-
.../USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr | 2 +-
.../USER/lb/confined_colloid/in.confined_colloids | 108 +
.../LAMMPS/USER/lb/confined_colloid/results64.out | 41 +
.../LAMMPS/USER/lb/dragforce/data.one_radius16d2 | 330 +
.../LAMMPS/USER/lb/dragforce/defaultgamma_drag.out | 10035 ++
.../LAMMPS/USER/lb/dragforce/in.defaultgamma_drag | 80 +
examples/LAMMPS/USER/lb/dragforce/in.setgamma_drag | 68 +
.../LAMMPS/USER/lb/dragforce/setgamma13d0_drag.out | 10035 ++
examples/LAMMPS/USER/lb/fourspheres/data.four | 1290 +
.../fourspheres_velocity0d0001_defaultgamma.out | 15039 +++
.../fourspheres_velocity0d0001_setgamma.out | 15039 +++
.../lb/fourspheres/in.fourspheres_default_gamma | 84 +
.../USER/lb/fourspheres/in.fourspheres_set_gamma | 76 +
examples/LAMMPS/USER/lb/microrheology/data.two | 492 +
.../microrheology/in.microrheology_default_gamma | 119 +
.../lb/microrheology/in.microrheology_set_gamma | 113 +
.../microrheology/microrheology_defaultgamma.out | 50000 +++++++++
.../lb/microrheology/microrheology_setgamma.out | 50000 +++++++++
.../LAMMPS/USER/lb/planewall/data.one_radius16d2 | 330 +
.../USER/lb/planewall/in.planewall_default_gamma | 99 +
.../USER/lb/planewall/in.planewall_set_gamma | 92 +
.../LAMMPS/USER/lb/planewall/wall_defaultgamma.out | 20031 ++++
.../LAMMPS/USER/lb/planewall/wall_setgamma.out | 20031 ++++
examples/LAMMPS/USER/lb/polymer/data.polymer | 1040 +
examples/LAMMPS/USER/lb/polymer/in.polymer | 105 +
examples/LAMMPS/USER/lb/polymer/out.polymer | 19 +
examples/LAMMPS/USER/misc/basal/almg.liu | 708 +
examples/LAMMPS/USER/misc/basal/in.basal | 163 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/bcc.in | 33 +
.../USER/misc/meam_sw_spline/Si/bcc_relax.in | 37 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/dc.in | 34 +
.../LAMMPS/USER/misc/meam_sw_spline/Si/dc_relax.in | 38 +
.../Si/energy_conservation.meam.sw.in | 45 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/fcc.in | 34 +
.../USER/misc/meam_sw_spline/Si/fcc_relax.in | 38 +
.../USER/misc/meam_sw_spline/Si/hcp_relax.in | 40 +
examples/LAMMPS/USER/misc/meam_sw_spline/Si/sc.in | 34 +
.../LAMMPS/USER/misc/meam_sw_spline/Si/sc_relax.in | 38 +
.../USER/misc/meam_sw_spline/Si/single_atom.in | 27 +
.../LAMMPS/USER/misc/meam_sw_spline/Ti/alpha.in | 27 +
.../misc/meam_sw_spline/Ti/alpha_relaxation.in | 38 +
.../LAMMPS/USER/misc/meam_sw_spline/Ti/beta.in | 27 +
.../Ti/energy_conservation.meam.sw.in | 74 +
examples/LAMMPS/USER/misc/meam_sw_spline/Ti/fcc.in | 28 +
.../USER/misc/meam_sw_spline/Ti/hexagonal.in | 28 +
.../LAMMPS/USER/misc/meam_sw_spline/Ti/omega.in | 27 +
.../USER/misc/meam_sw_spline/Ti/single_atom.in | 27 +
examples/LAMMPS/USER/misc/ti/in.ti_rs | 64 +
examples/LAMMPS/USER/misc/ti/in.ti_spring | 64 +
examples/LAMMPS/USER/phonon/1-1D-mono/README | 39 +
examples/LAMMPS/USER/phonon/1-1D-mono/data.pos | 57 +
examples/LAMMPS/USER/phonon/1-1D-mono/disp.dat | 19 +
examples/LAMMPS/USER/phonon/1-1D-mono/in.Ana | 50 +
examples/LAMMPS/USER/phonon/1-1D-mono/in.disp | 9 +
.../USER/phonon/1-1D-mono/log.lammps.example | 146 +
examples/LAMMPS/USER/phonon/1-1D-mono/map.in | 18 +
examples/LAMMPS/USER/phonon/1-1D-mono/pdisp.eps | 776 +
.../USER/phonon/1-1D-mono/phonon.bin.2000000 | Bin 0 -> 384 bytes
examples/LAMMPS/USER/phonon/1-1D-mono/phonon.log | 110 +
examples/LAMMPS/USER/phonon/1-1D-mono/plot.disp | 20 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/README | 37 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/data.pos | 154 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/disp.dat | 35 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/in.Ana | 46 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/in.disp | 9 +
.../USER/phonon/2-1D-diatomic/log.lammps.example | 113 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/map.in | 66 +
.../LAMMPS/USER/phonon/2-1D-diatomic/pdisp.eps | 924 +
examples/LAMMPS/USER/phonon/2-1D-diatomic/pdos.dat | 203 +
.../USER/phonon/2-1D-diatomic/phonon.bin.2000000 | Bin 0 -> 2196 bytes
.../LAMMPS/USER/phonon/2-1D-diatomic/phonon.log | 206 +
.../LAMMPS/USER/phonon/2-1D-diatomic/plot.disp | 25 +
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000 | Bin 0 -> 73872 bytes
.../phonon/3-3D-FCC-Cu-EAM/CuPhonon.log.example | 1575 +
examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/README | 47 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam | 0
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/data.pos | 524 +
.../USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat | 83 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat | 86 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat | 47 +
.../USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat | 164 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat | 101 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat | 102 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D | 40 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.disp | 21 +
examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.dos | 11 +
.../USER/phonon/3-3D-FCC-Cu-EAM/log.lammps.example | 107 +
examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/map.in | 514 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps | 1207 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps | 985 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp | 18 +
.../LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos | 13 +
.../USER/sph/water_collapse/water_collapse.lmp | 4 +-
examples/LAMMPS/VISCOSITY/README | 80 +
examples/LAMMPS/VISCOSITY/in.gk.2d | 65 +
examples/LAMMPS/VISCOSITY/in.mp.2d | 76 +
examples/LAMMPS/VISCOSITY/in.nemd.2d | 83 +
examples/LAMMPS/VISCOSITY/in.wall.2d | 83 +
examples/LAMMPS/VISCOSITY/log.gk.2d.12Sep13 | 386 +
examples/LAMMPS/VISCOSITY/log.mp.2d.12Sep13 | 231 +
examples/LAMMPS/VISCOSITY/log.nemd.2d.12Sep13 | 264 +
examples/LAMMPS/VISCOSITY/log.wall.2d.12Sep13 | 216 +
examples/LAMMPS/VISCOSITY/profile.gk.2d.12Sep13 | 100654 ++++++++++++++++++
examples/LAMMPS/VISCOSITY/profile.mp.2d.12Sep13 | 1473 +
examples/LAMMPS/VISCOSITY/profile.nemd.2d.12Sep13 | 318 +
examples/LAMMPS/VISCOSITY/profile.wall.2d.12Sep13 | 66 +
examples/LAMMPS/body/data.body | 549 +
examples/LAMMPS/body/in.body | 23 +
examples/LAMMPS/body/log.body.18Feb13.linux.1 | 70 +
examples/LAMMPS/body/log.body.18Feb13.linux.4 | 70 +
.../LAMMPS/colloid/log.colloid.18Feb13.linux.1 | 125 +
.../LAMMPS/colloid/log.colloid.18Feb13.linux.4 | 125 +
examples/LAMMPS/colloid/log.colloid.9Jan12.linux.1 | 122 -
examples/LAMMPS/colloid/log.colloid.9Jan12.linux.4 | 122 -
examples/LAMMPS/comb/data.comb3-OHCCu | 695 +
examples/LAMMPS/comb/ffield.comb3 | 349 +
examples/LAMMPS/comb/in.comb.Si.elastic | 2 +-
examples/LAMMPS/comb/in.comb3 | 34 +
examples/LAMMPS/comb/lib.comb3 | 24303 +++++
examples/LAMMPS/comb/log.comb.Cu.18Feb13.linux.1 | 73 +
examples/LAMMPS/comb/log.comb.Cu.18Feb13.linux.4 | 73 +
examples/LAMMPS/comb/log.comb.Cu.9Jan12.linux.1 | 69 -
examples/LAMMPS/comb/log.comb.Cu.9Jan12.linux.4 | 69 -
.../comb/log.comb.Cu2O.elastic.18Feb13.linux.1 | 315 +
.../comb/log.comb.Cu2O.elastic.18Feb13.linux.4 | 315 +
.../comb/log.comb.Cu2O.elastic.9Jan12.linux.1 | 340 -
.../comb/log.comb.Cu2O.elastic.9Jan12.linux.4 | 342 -
examples/LAMMPS/comb/log.comb.CuaS.9Jan12.linux.1 | 41 -
examples/LAMMPS/comb/log.comb.CuaS.9Jan12.linux.4 | 41 -
examples/LAMMPS/comb/log.comb.HfO2.18Feb13.linux.1 | 259 +
examples/LAMMPS/comb/log.comb.HfO2.18Feb13.linux.4 | 259 +
examples/LAMMPS/comb/log.comb.HfO2.9Jan12.linux.1 | 193 -
examples/LAMMPS/comb/log.comb.HfO2.9Jan12.linux.4 | 291 -
examples/LAMMPS/comb/log.comb.Si.18Feb13.linux.1 | 73 +
examples/LAMMPS/comb/log.comb.Si.18Feb13.linux.4 | 73 +
examples/LAMMPS/comb/log.comb.Si.9Jan12.linux.1 | 69 -
examples/LAMMPS/comb/log.comb.Si.9Jan12.linux.4 | 69 -
.../comb/log.comb.Si.elastic.18Feb13.linux.1 | 274 +
.../comb/log.comb.Si.elastic.18Feb13.linux.4 | 274 +
.../LAMMPS/comb/log.comb.Si.elastic.9Jan12.linux.1 | 296 -
.../LAMMPS/comb/log.comb.Si.elastic.9Jan12.linux.4 | 296 -
examples/LAMMPS/comb/log.comb3.4Nov13.linux.1 | 72 +
examples/LAMMPS/comb/log.comb3.4Nov13.linux.4 | 72 +
examples/LAMMPS/crack/log.crack.18Feb13.linux.1 | 135 +
examples/LAMMPS/crack/log.crack.18Feb13.linux.4 | 135 +
examples/LAMMPS/crack/log.crack.9Jan12.linux.1 | 130 -
examples/LAMMPS/crack/log.crack.9Jan12.linux.4 | 130 -
examples/LAMMPS/dipole/in.dipole | 2 +-
examples/LAMMPS/dipole/log.dipole.18Feb13.linux.1 | 89 +
examples/LAMMPS/dipole/log.dipole.18Feb13.linux.4 | 89 +
examples/LAMMPS/dipole/log.dipole.9Jan12.linux.1 | 86 -
examples/LAMMPS/dipole/log.dipole.9Jan12.linux.4 | 86 -
.../LAMMPS/dreiding/log.dreiding.18Feb13.linux.1 | 98 +
.../LAMMPS/dreiding/log.dreiding.18Feb13.linux.4 | 98 +
.../LAMMPS/dreiding/log.dreiding.9Jan12.linux.1 | 97 -
.../LAMMPS/dreiding/log.dreiding.9Jan12.linux.4 | 121 -
examples/LAMMPS/eim/log.eim.18Feb13.linux.1 | 67 +
examples/LAMMPS/eim/log.eim.18Feb13.linux.4 | 67 +
examples/LAMMPS/eim/log.eim.9Jan12.linux.1 | 54 -
examples/LAMMPS/eim/log.eim.9Jan12.linux.4 | 54 -
examples/LAMMPS/ellipse/in.ellipse.gayberne | 4 +-
.../ellipse/log.ellipse.gayberne.18Feb13.linux.1 | 157 +
.../ellipse/log.ellipse.gayberne.18Feb13.linux.4 | 157 +
.../ellipse/log.ellipse.gayberne.9Jan12.linux.1 | 161 -
.../ellipse/log.ellipse.gayberne.9Jan12.linux.4 | 161 -
.../ellipse/log.ellipse.resquared.18Feb13.linux.1 | 157 +
.../ellipse/log.ellipse.resquared.18Feb13.linux.4 | 157 +
.../ellipse/log.ellipse.resquared.9Jan12.linux.1 | 161 -
.../ellipse/log.ellipse.resquared.9Jan12.linux.4 | 161 -
.../LAMMPS/flow/log.flow.couette.18Feb13.linux.1 | 127 +
.../LAMMPS/flow/log.flow.couette.18Feb13.linux.4 | 127 +
.../LAMMPS/flow/log.flow.couette.9Jan12.linux.1 | 123 -
.../LAMMPS/flow/log.flow.couette.9Jan12.linux.4 | 123 -
examples/LAMMPS/flow/log.flow.pois.18Feb13.linux.1 | 127 +
examples/LAMMPS/flow/log.flow.pois.18Feb13.linux.4 | 127 +
examples/LAMMPS/flow/log.flow.pois.9Jan12.linux.1 | 123 -
examples/LAMMPS/flow/log.flow.pois.9Jan12.linux.4 | 123 -
examples/LAMMPS/friction/in.friction | 1 +
.../LAMMPS/friction/log.friction.18Feb13.linux.1 | 145 +
.../LAMMPS/friction/log.friction.18Feb13.linux.4 | 145 +
.../LAMMPS/friction/log.friction.9Jan12.linux.1 | 141 -
.../LAMMPS/friction/log.friction.9Jan12.linux.4 | 141 -
.../LAMMPS/gpu/log.gpu.melt.2.5.18Feb13.linux.1 | 77 +
.../LAMMPS/gpu/log.gpu.melt.2.5.18Feb13.linux.4 | 77 +
.../LAMMPS/gpu/log.gpu.melt.2.5.9Jan12.linux.1 | 77 -
.../LAMMPS/gpu/log.gpu.melt.2.5.9Jan12.linux.4 | 77 -
.../LAMMPS/gpu/log.gpu.melt.5.0.18Feb13.linux.1 | 77 +
.../LAMMPS/gpu/log.gpu.melt.5.0.18Feb13.linux.4 | 77 +
.../LAMMPS/gpu/log.gpu.melt.5.0.9Jan12.linux.1 | 77 -
.../LAMMPS/gpu/log.gpu.melt.5.0.9Jan12.linux.4 | 77 -
.../LAMMPS/gpu/log.gpu.phosphate.18Feb13.linux.1 | 75 +
.../LAMMPS/gpu/log.gpu.phosphate.18Feb13.linux.4 | 75 +
.../LAMMPS/gpu/log.gpu.phosphate.9Jan12.linux.1 | 74 -
.../LAMMPS/gpu/log.gpu.phosphate.9Jan12.linux.4 | 74 -
examples/LAMMPS/gpu/log.gpu.rhodo.18Feb13.linux.1 | 122 +
examples/LAMMPS/gpu/log.gpu.rhodo.18Feb13.linux.4 | 122 +
examples/LAMMPS/gpu/log.gpu.rhodo.9Jan12.linux.1 | 121 -
examples/LAMMPS/gpu/log.gpu.rhodo.9Jan12.linux.4 | 121 -
.../hugoniostat/log.hugoniostat.18Feb13.linux.1 | 90 +
.../hugoniostat/log.hugoniostat.18Feb13.linux.4 | 90 +
.../hugoniostat/log.hugoniostat.9Jan12.linux.1 | 90 -
.../hugoniostat/log.hugoniostat.9Jan12.linux.4 | 90 -
examples/LAMMPS/indent/log.indent.18Feb13.linux.1 | 176 +
examples/LAMMPS/indent/log.indent.18Feb13.linux.4 | 176 +
examples/LAMMPS/indent/log.indent.9Jan12.linux.1 | 172 -
examples/LAMMPS/indent/log.indent.9Jan12.linux.4 | 172 -
.../LAMMPS/indent/log.indent.min.18Feb13.linux.1 | 386 +
.../LAMMPS/indent/log.indent.min.18Feb13.linux.4 | 383 +
.../LAMMPS/indent/log.indent.min.9Jan12.linux.1 | 404 -
.../LAMMPS/indent/log.indent.min.9Jan12.linux.4 | 386 -
examples/LAMMPS/kim/in.kim.lj | 4 +-
examples/LAMMPS/kim/in.kim.lj.lmp | 4 +-
examples/LAMMPS/kim/log.kim.lj.26Jul13.mac_mpi.1 | 29 +
examples/LAMMPS/kim/log.kim.lj.26Jul13.mac_mpi.4 | 29 +
examples/LAMMPS/kim/log.kim.lj.9Jan12.linux.1 | 71 -
examples/LAMMPS/kim/log.kim.lj.9Jan12.linux.4 | 71 -
.../LAMMPS/kim/log.kim.lj.lmp.26Jul13.mac_mpi.1 | 29 +
.../LAMMPS/kim/log.kim.lj.lmp.26Jul13.mac_mpi.4 | 29 +
examples/LAMMPS/kim/log.kim.lj.lmp.9Jan12.linux.1 | 71 -
examples/LAMMPS/kim/log.kim.lj.lmp.9Jan12.linux.4 | 71 -
examples/LAMMPS/meam/log.meam.18Feb13.linux.1 | 63 +
examples/LAMMPS/meam/log.meam.18Feb13.linux.4 | 63 +
examples/LAMMPS/meam/log.meam.9Jan12.linux.1 | 60 -
examples/LAMMPS/meam/log.meam.9Jan12.linux.4 | 60 -
.../LAMMPS/meam/log.meam.shear.18Feb13.linux.1 | 169 +
.../LAMMPS/meam/log.meam.shear.18Feb13.linux.4 | 169 +
examples/LAMMPS/meam/log.meam.shear.9Jan12.linux.1 | 165 -
examples/LAMMPS/meam/log.meam.shear.9Jan12.linux.4 | 165 -
examples/LAMMPS/melt/log.melt.18Feb13.linux.1 | 60 +
examples/LAMMPS/melt/log.melt.18Feb13.linux.4 | 60 +
examples/LAMMPS/melt/log.melt.9Jan12.linux.1 | 57 -
examples/LAMMPS/melt/log.melt.9Jan12.linux.4 | 57 -
.../LAMMPS/micelle/log.micelle.18Feb13.linux.1 | 209 +
.../LAMMPS/micelle/log.micelle.18Feb13.linux.4 | 209 +
examples/LAMMPS/micelle/log.micelle.9Jan12.linux.1 | 205 -
examples/LAMMPS/micelle/log.micelle.9Jan12.linux.4 | 205 -
examples/LAMMPS/min/log.min.18Feb13.linux.1 | 115 +
examples/LAMMPS/min/log.min.18Feb13.linux.4 | 115 +
examples/LAMMPS/min/log.min.9Jan12.linux.1 | 111 -
examples/LAMMPS/min/log.min.9Jan12.linux.4 | 111 -
examples/LAMMPS/min/log.min.box.18Feb13.linux.1 | 353 +
examples/LAMMPS/min/log.min.box.18Feb13.linux.4 | 353 +
examples/LAMMPS/min/log.min.box.9Jan12.linux.1 | 352 -
examples/LAMMPS/min/log.min.box.9Jan12.linux.4 | 352 -
examples/LAMMPS/msst/log.msst.18Feb13.linux.1 | 135 +
examples/LAMMPS/msst/log.msst.18Feb13.linux.4 | 135 +
examples/LAMMPS/msst/log.msst.9Jan12.linux.1 | 130 -
examples/LAMMPS/msst/log.msst.9Jan12.linux.4 | 130 -
examples/LAMMPS/neb/final.hop1 | 1 +
examples/LAMMPS/neb/final.hop2 | 1 +
examples/LAMMPS/neb/log.neb.hop1.18Feb13.linux.4 | 11 +
examples/LAMMPS/neb/log.neb.hop1.9Jan12.linux.4 | 11 -
examples/LAMMPS/neb/log.neb.hop2.18Feb13.linux.4 | 19 +
examples/LAMMPS/neb/log.neb.hop2.9Jan12.linux.4 | 19 -
examples/LAMMPS/nemd/in.nemd | 2 +-
examples/LAMMPS/nemd/log.nemd.18Feb13.linux.1 | 112 +
examples/LAMMPS/nemd/log.nemd.18Feb13.linux.4 | 112 +
examples/LAMMPS/nemd/log.nemd.9Jan12.linux.1 | 109 -
examples/LAMMPS/nemd/log.nemd.9Jan12.linux.4 | 109 -
.../LAMMPS/obstacle/log.obstacle.18Feb13.linux.1 | 137 +
.../LAMMPS/obstacle/log.obstacle.18Feb13.linux.4 | 137 +
.../LAMMPS/obstacle/log.obstacle.9Jan12.linux.1 | 135 -
.../LAMMPS/obstacle/log.obstacle.9Jan12.linux.4 | 135 -
examples/LAMMPS/peptide/in.peptide | 2 +-
.../LAMMPS/peptide/log.peptide.18Feb13.linux.1 | 164 +
.../LAMMPS/peptide/log.peptide.18Feb13.linux.4 | 164 +
examples/LAMMPS/peptide/log.peptide.9Jan12.linux.1 | 159 -
examples/LAMMPS/peptide/log.peptide.9Jan12.linux.4 | 159 -
examples/LAMMPS/peri/log.peri.18Feb13.linux.1 | 84 +
examples/LAMMPS/peri/log.peri.18Feb13.linux.4 | 84 +
examples/LAMMPS/peri/log.peri.9Jan12.linux.1 | 81 -
examples/LAMMPS/peri/log.peri.9Jan12.linux.4 | 81 -
examples/LAMMPS/prd/log.prd.0.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.0.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.1.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.1.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.18Feb13.linux.4 | 12 +
examples/LAMMPS/prd/log.prd.2.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.2.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.3.18Feb13.linux.4 | 631 +
examples/LAMMPS/prd/log.prd.3.9Jan12.linux.4 | 630 -
examples/LAMMPS/prd/log.prd.9Jan12.linux.4 | 12 -
examples/LAMMPS/reax/AB/in.AB | 2 +-
examples/LAMMPS/reax/Au_O/in.AuO | 2 +-
examples/LAMMPS/reax/CHO/in.CHO | 2 +-
examples/LAMMPS/reax/Fe_O_H/in.FeOH3 | 2 +-
examples/LAMMPS/reax/Fluorographene/README | 13 +
examples/LAMMPS/reax/Fluorographene/data.FC | 17296 +++
examples/LAMMPS/reax/Fluorographene/dumpnpt.xyz | 17282 +++
examples/LAMMPS/reax/Fluorographene/ffield.reax.FC | 361 +
examples/LAMMPS/reax/Fluorographene/in.FC | 32 +
examples/LAMMPS/reax/Fluorographene/log.FC | 290 +
examples/LAMMPS/reax/RDX/in.RDX | 2 +-
examples/LAMMPS/reax/README | 49 +-
examples/LAMMPS/reax/V_O_H/in.VOH | 2 +-
examples/LAMMPS/reax/Zn_O_H/ffield.reax.ZnOH | 2 +-
examples/LAMMPS/reax/Zn_O_H/in.ZnOH2 | 2 +-
examples/LAMMPS/reax/in.reaxc.rdx | 2 +-
examples/LAMMPS/reax/in.reaxc.tatb | 6 +-
examples/LAMMPS/reax/log.reax.rdx.18Feb13.linux.1 | 81 +
examples/LAMMPS/reax/log.reax.rdx.18Feb13.linux.4 | 81 +
examples/LAMMPS/reax/log.reax.rdx.9Jan12.linux.1 | 170 -
examples/LAMMPS/reax/log.reax.rdx.9Jan12.linux.4 | 170 -
examples/LAMMPS/reax/log.reax.tatb.18Feb13.linux.1 | 77 +
examples/LAMMPS/reax/log.reax.tatb.18Feb13.linux.4 | 77 +
examples/LAMMPS/reax/log.reax.tatb.9Jan12.linux.1 | 97 -
examples/LAMMPS/reax/log.reax.tatb.9Jan12.linux.4 | 97 -
examples/LAMMPS/reax/log.reaxc.rdx.18Feb13.linux.1 | 81 +
examples/LAMMPS/reax/log.reaxc.rdx.18Feb13.linux.4 | 81 +
examples/LAMMPS/reax/log.reaxc.rdx.9Jan12.linux.1 | 78 -
examples/LAMMPS/reax/log.reaxc.rdx.9Jan12.linux.4 | 78 -
.../LAMMPS/reax/log.reaxc.tatb.18Feb13.linux.1 | 79 +
.../LAMMPS/reax/log.reaxc.tatb.18Feb13.linux.4 | 79 +
examples/LAMMPS/reax/log.reaxc.tatb.9Jan12.linux.1 | 95 -
examples/LAMMPS/reax/log.reaxc.tatb.9Jan12.linux.4 | 95 -
examples/LAMMPS/rigid/data.rigid.tnr | 7220 ++
examples/LAMMPS/rigid/in.rigid.tnr | 89 +
examples/LAMMPS/rigid/log.rigid.18Feb13.linux.1 | 310 +
examples/LAMMPS/rigid/log.rigid.18Feb13.linux.4 | 310 +
examples/LAMMPS/rigid/log.rigid.9Jan12.linux.1 | 306 -
examples/LAMMPS/rigid/log.rigid.9Jan12.linux.4 | 306 -
.../LAMMPS/rigid/log.rigid.poems.18Feb13.linux.1 | 310 +
.../LAMMPS/rigid/log.rigid.poems.18Feb13.linux.4 | 310 +
.../LAMMPS/rigid/log.rigid.poems.9Jan12.linux.1 | 306 -
.../LAMMPS/rigid/log.rigid.poems.9Jan12.linux.4 | 306 -
.../LAMMPS/rigid/log.rigid.poems2.18Feb13.linux.1 | 314 +
.../LAMMPS/rigid/log.rigid.poems2.18Feb13.linux.4 | 314 +
.../LAMMPS/rigid/log.rigid.poems2.9Jan12.linux.1 | 310 -
.../LAMMPS/rigid/log.rigid.poems2.9Jan12.linux.4 | 310 -
examples/LAMMPS/shear/log.shear.18Feb13.linux.1 | 165 +
examples/LAMMPS/shear/log.shear.18Feb13.linux.4 | 165 +
examples/LAMMPS/shear/log.shear.9Jan12.linux.1 | 161 -
examples/LAMMPS/shear/log.shear.9Jan12.linux.4 | 161 -
.../LAMMPS/shear/log.shear.void.18Feb13.linux.1 | 166 +
.../LAMMPS/shear/log.shear.void.18Feb13.linux.4 | 166 +
.../LAMMPS/shear/log.shear.void.9Jan12.linux.1 | 162 -
.../LAMMPS/shear/log.shear.void.9Jan12.linux.4 | 162 -
examples/LAMMPS/srd/in.srd.mixture | 1 -
.../LAMMPS/srd/log.srd.mixture.18Feb13.linux.1 | 142 +
.../LAMMPS/srd/log.srd.mixture.18Feb13.linux.4 | 142 +
examples/LAMMPS/srd/log.srd.mixture.9Jan12.linux.1 | 223 -
examples/LAMMPS/srd/log.srd.mixture.9Jan12.linux.4 | 223 -
examples/LAMMPS/srd/log.srd.pure.18Feb13.linux.1 | 592 +
examples/LAMMPS/srd/log.srd.pure.18Feb13.linux.4 | 592 +
examples/LAMMPS/srd/log.srd.pure.9Jan12.linux.1 | 138 -
examples/LAMMPS/srd/log.srd.pure.9Jan12.linux.4 | 138 -
examples/LAMMPS/tad/log.tad.0.18Feb13.linux.3 | 12877 +++
examples/LAMMPS/tad/log.tad.0.9Jan12.linux.3 | 7530 --
examples/LAMMPS/tad/log.tad.1.18Feb13.linux.3 | 7814 ++
examples/LAMMPS/tad/log.tad.1.9Jan12.linux.3 | 2868 -
examples/LAMMPS/tad/log.tad.18Feb13.linux.3 | 114 +
examples/LAMMPS/tad/log.tad.2.18Feb13.linux.3 | 7814 ++
examples/LAMMPS/tad/log.tad.2.9Jan12.linux.3 | 2868 -
examples/LAMMPS/tad/log.tad.9Jan12.linux.3 | 39 -
examples/LAMMPS/tad/log.tad.neb.18Feb13.linux.3 | 1423 +
examples/LAMMPS/tad/log.tad.neb.9Jan12.linux.3 | 487 -
examples/LAMMPS/voronoi/in.voronoi | 154 +
examples/LAMMPS/voronoi/log.voronoi.4Aug13.macos.1 | 368 +
examples/LAMMPS/voronoi/log.voronoi.4Aug13.macos.4 | 368 +
.../Tutorials_public/chute_wear/in.chute_wear | 8 +-
.../chute_wear/{ => meshes}/insertion_face.stl | 0
.../chute_wear/{ => meshes}/simple_chute.stl | 0
.../post/dummy => chute_wear/post/.gitignore} | 0
.../Tutorials_public/chute_wear/post/dummy | 1 -
.../Tutorials_public/chute_wear/postscript | 2 +-
.../Tutorials_public/chute_wear/run.config | 9 +
.../LIGGGHTS/Tutorials_public/cohesion/in.cohesion | 8 +-
.../Tutorials_public/cohesion/in.noCohesion | 8 +-
.../post/dummy => cohesion/post/.gitignore} | 0
.../LIGGGHTS/Tutorials_public/cohesion/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/cohesion/run.config | 14 +
.../Tutorials_public/contactModels/in.newModels | 8 +-
.../Tutorials_public/contactModels/in.oldModels | 2 +-
.../Tutorials_public/contactModels/post/.gitignore | 0
.../Tutorials_public/contactModels/post/dummy | 1 -
.../Tutorials_public/contactModels/run.config | 9 +
.../LIGGGHTS/Tutorials_public/conveyor/in.conveyor | 10 +-
.../Tutorials_public/conveyor/{ => meshes}/box.stl | 0
.../conveyor/{ => meshes}/conveyor.stl | 0
.../conveyor/{ => meshes}/insertion_face.stl | 0
.../Tutorials_public/conveyor/post/.gitignore | 0
.../LIGGGHTS/Tutorials_public/conveyor/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/conveyor/run.config | 9 +
.../Tutorials_public/heatTransfer_1/in.heatGran | 8 +-
.../heatTransfer_1/post/.gitignore | 0
.../Tutorials_public/heatTransfer_1/post/dummy | 1 -
.../Tutorials_public/heatTransfer_1/run.config | 9 +
.../LIGGGHTS/Tutorials_public/heatTransfer_2/LOG | 896 -
.../Tutorials_public/heatTransfer_2/in.heatGran | 8 +-
.../heatTransfer_2/post/.gitignore | 0
.../Tutorials_public/heatTransfer_2/post/dummy | 1 -
.../Tutorials_public/heatTransfer_2/run.config | 9 +
.../Tutorials_public/hysteresis/in.hysteresis | 8 +-
.../Tutorials_public/hysteresis/in.noHysteresis | 8 +-
.../Tutorials_public/hysteresis/post/.gitignore | 0
.../Tutorials_public/hysteresis/post/dummy | 1 -
.../Tutorials_public/hysteresis/run.config | 14 +
.../insert_stream/in.insert_stream | 8 +-
.../insert_stream/in.insert_stream_reset_timestep | 69 +
.../insert_stream/{ => meshes}/face.stl | 0
.../Tutorials_public/insert_stream/post.py | 3 -
.../Tutorials_public/insert_stream/post/.gitignore | 0
.../Tutorials_public/insert_stream/post/dummy | 1 -
.../Tutorials_public/insert_stream/run.config | 9 +
.../Tutorials_public/insert_stream/state.pvsm | 3870 -
.../LIGGGHTS/Tutorials_public/meshGran/in.meshGran | 8 +-
.../meshGran/{ => meshes}/insertion_face.stl | 0
.../meshGran/{ => meshes}/mesh.stl | 0
.../Tutorials_public/meshGran/post/.gitignore | 0
.../LIGGGHTS/Tutorials_public/meshGran/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/meshGran/run.config | 9 +
.../Tutorials_public/mesh_tet/{ => data}/test.vtk | 0
.../LIGGGHTS/Tutorials_public/mesh_tet/in.mesh_tet | 4 +-
.../Tutorials_public/mesh_tet/log.liggghts | 120 -
.../Tutorials_public/mesh_tet/post/.gitignore | 0
.../LIGGGHTS/Tutorials_public/mesh_tet/run.config | 9 +
.../LIGGGHTS/Tutorials_public/mesh_tet/runscript | 2 +-
.../movingMeshGran/in.movingMeshGran | 18 +-
.../movingMeshGran/{ => meshes}/bucket.stl | 0
.../Tutorials_public/movingMeshGran/post.py | 3 -
.../movingMeshGran/post/.gitignore | 0
.../Tutorials_public/movingMeshGran/post/dummy | 1 -
.../Tutorials_public/movingMeshGran/run.config | 9 +
.../LIGGGHTS/Tutorials_public/packing/in.packing | 14 +-
.../LIGGGHTS/Tutorials_public/packing/log.liggghts | 246 -
.../Tutorials_public/packing/post/.gitignore | 0
.../LIGGGHTS/Tutorials_public/packing/run.config | 9 +
.../Tutorials_public/sph_1/post/.gitignore | 0
.../LIGGGHTS/Tutorials_public/sph_1/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/sph_1/run.config | 9 +
.../Tutorials_public/sph_2/post/.gitignore | 0
.../LIGGGHTS/Tutorials_public/sph_2/post/dummy | 1 -
.../LIGGGHTS/Tutorials_public/sph_2/run.config | 9 +
lib/atc/ATC_Coupling.cpp | 2215 +
lib/atc/ATC_Coupling.h | 456 +
lib/atc/ATC_CouplingEnergy.cpp | 412 +
lib/atc/ATC_CouplingEnergy.h | 82 +
lib/atc/ATC_CouplingMass.cpp | 285 +
lib/atc/ATC_CouplingMass.h | 88 +
lib/atc/ATC_CouplingMomentum.cpp | 453 +
lib/atc/ATC_CouplingMomentum.h | 84 +
lib/atc/ATC_CouplingMomentumEnergy.cpp | 508 +
lib/atc/ATC_CouplingMomentumEnergy.h | 83 +
lib/atc/ATC_Error.h | 44 +-
lib/atc/ATC_HardyKernel.cpp | 386 -
lib/atc/ATC_HardyKernel.h | 127 -
lib/atc/ATC_Method.cpp | 2310 +
lib/atc/ATC_Method.h | 863 +
lib/atc/ATC_Transfer.cpp | 2956 +-
lib/atc/ATC_Transfer.h | 1134 +-
lib/atc/ATC_TransferHardy.cpp | 2230 -
lib/atc/ATC_TransferHardy.h | 346 -
lib/atc/ATC_TransferKernel.cpp | 485 +
lib/atc/ATC_TransferKernel.h | 53 +
lib/atc/ATC_TransferPartitionOfUnity.cpp | 506 +
lib/atc/ATC_TransferPartitionOfUnity.h | 59 +
lib/atc/ATC_TransferThermal.cpp | 541 -
lib/atc/ATC_TransferThermal.h | 96 -
lib/atc/ATC_TransferUtility.cpp | 2221 -
lib/atc/ATC_TypeDefs.h | 621 +-
lib/atc/Array.h | 214 +-
lib/atc/Array2D.h | 26 +-
lib/atc/AtomToMoleculeTransfer.cpp | 225 +
lib/atc/AtomToMoleculeTransfer.h | 239 +
lib/atc/AtomicRegulator.cpp | 830 +-
lib/atc/AtomicRegulator.h | 411 +-
lib/atc/BodyForce.cpp | 37 +
lib/atc/BodyForce.h | 68 +
lib/atc/CBLattice.cpp | 204 +
lib/atc/CBLattice.h | 97 +
lib/atc/CG.h | 7 +-
lib/atc/CauchyBorn.cpp | 572 +
lib/atc/CauchyBorn.h | 113 +
lib/atc/CbEam.h | 209 +
lib/atc/CbLjCut.h | 62 +
lib/atc/CbLjSmoothLinear.h | 88 +
lib/atc/CbPotential.cpp | 88 +
lib/atc/CbPotential.h | 70 +
lib/atc/ChargeRegulator.cpp | 735 +
lib/atc/ChargeRegulator.h | 282 +
lib/atc/CloneVector.h | 44 +-
lib/atc/ConcentrationRegulator.cpp | 635 +
lib/atc/ConcentrationRegulator.h | 216 +
lib/atc/DenseMatrix.h | 146 +-
lib/atc/DenseVector.h | 28 +-
lib/atc/DependencyManager.h | 326 +
lib/atc/DiagonalMatrix.h | 94 +-
lib/atc/DislocationExtractor.h | 434 +
lib/atc/ElasticTimeIntegrator.cpp | 796 +-
lib/atc/ElasticTimeIntegrator.h | 420 +-
lib/atc/ElectronChargeDensity.cpp | 131 +
lib/atc/ElectronChargeDensity.h | 269 +
lib/atc/ElectronDragPower.cpp | 75 +
lib/atc/ElectronDragPower.h | 71 +
lib/atc/ElectronFlux.cpp | 51 +-
lib/atc/ElectronFlux.h | 242 +-
lib/atc/ElectronHeatCapacity.cpp | 40 +-
lib/atc/ElectronHeatCapacity.h | 209 +-
lib/atc/ElectronHeatFlux.cpp | 59 +-
lib/atc/ElectronHeatFlux.h | 184 +-
lib/atc/ElectronPhononExchange.cpp | 79 +-
lib/atc/ElectronPhononExchange.h | 107 +-
lib/atc/ExtrinsicModel.cpp | 151 +-
lib/atc/ExtrinsicModel.h | 143 +-
lib/atc/ExtrinsicModelDriftDiffusion.cpp | 558 +
lib/atc/ExtrinsicModelDriftDiffusion.h | 187 +
lib/atc/ExtrinsicModelElectrostatic.cpp | 1014 +
lib/atc/ExtrinsicModelElectrostatic.h | 187 +
lib/atc/ExtrinsicModelTwoTemperature.cpp | 61 +-
lib/atc/ExtrinsicModelTwoTemperature.h | 15 +-
lib/atc/FE_Element.cpp | 1084 +-
lib/atc/FE_Element.h | 369 +-
lib/atc/FE_Engine.cpp | 3221 +-
lib/atc/FE_Engine.h | 598 +-
lib/atc/FE_Interpolate.cpp | 993 +
lib/atc/FE_Interpolate.h | 263 +
lib/atc/FE_Mesh.cpp | 2520 +-
lib/atc/FE_Mesh.h | 607 +-
lib/atc/FE_Quadrature.h | 709 +
lib/atc/FieldEulerIntegrator.cpp | 41 +-
lib/atc/FieldEulerIntegrator.h | 12 +-
lib/atc/FieldManager.cpp | 548 +
lib/atc/FieldManager.h | 132 +
lib/atc/Function.cpp | 548 +
lib/atc/Function.h | 428 +
lib/atc/FundamentalAtomicQuantity.cpp | 152 +
lib/atc/FundamentalAtomicQuantity.h | 254 +
lib/atc/GMRES.h | 11 +-
lib/atc/GhostManager.cpp | 504 +
lib/atc/GhostManager.h | 327 +
lib/atc/ImplicitSolveOperator.cpp | 54 +-
lib/atc/ImplicitSolveOperator.h | 20 +-
lib/atc/InterscaleOperators.cpp | 666 +
lib/atc/InterscaleOperators.h | 465 +
lib/atc/KD_Tree.cpp | 164 +
lib/atc/KD_Tree.h | 89 +
lib/atc/KernelFunction.cpp | 726 +
lib/atc/KernelFunction.h | 255 +
lib/atc/KinetoThermostat.cpp | 436 +
lib/atc/KinetoThermostat.h | 689 +
lib/atc/Kinetostat.cpp | 2040 +-
lib/atc/Kinetostat.h | 603 +-
lib/atc/LammpsInterface.cpp | 1248 +-
lib/atc/LammpsInterface.h | 695 +-
lib/atc/LinearSolver.cpp | 563 +
lib/atc/LinearSolver.h | 182 +
lib/atc/MPI_Wrappers.cpp | 333 +
lib/atc/MPI_Wrappers.h | 45 +
lib/atc/Makefile.g++ | 98 +-
lib/atc/Makefile.icc | 96 +-
lib/atc/Makefile.lammps.empty | 5 +
.../{Makefile.lammps => Makefile.lammps.installed} | 0
lib/atc/Makefile.lammps.linalg | 6 +
lib/atc/Makefile.mingw32-cross | 66 +
lib/atc/Makefile.mingw32-cross-mpi | 67 +
lib/atc/Makefile.mingw64-cross | 66 +
lib/atc/Makefile.mingw64-cross-mpi | 67 +
lib/atc/Makefile.mpic++ | 29 +
lib/atc/Makefile.serial | 96 +-
lib/atc/Material.cpp | 647 +-
lib/atc/Material.h | 193 +-
lib/atc/Matrix.cpp | 183 +-
lib/atc/Matrix.h | 515 +-
lib/atc/MatrixDef.h | 78 +-
lib/atc/MatrixLibrary.h | 11 +-
lib/atc/MeshReader.cpp | 223 +
lib/atc/MeshReader.h | 52 +
lib/atc/MoleculeSet.cpp | 292 +
lib/atc/MoleculeSet.h | 158 +
lib/atc/NonLinearSolver.cpp | 114 +
lib/atc/NonLinearSolver.h | 105 +
lib/atc/OutputManager.cpp | 553 +-
lib/atc/OutputManager.h | 79 +-
lib/atc/PaqAtcUtility.cpp | 89 +
lib/atc/PaqAtcUtility.h | 65 +
lib/atc/ParDenseMatrix.h | 172 +
lib/atc/ParDiagonalMatrix.cpp | 93 +
lib/atc/ParDiagonalMatrix.h | 38 +
lib/atc/ParSparseMatrix.cpp | 302 +
lib/atc/ParSparseMatrix.h | 150 +
lib/atc/PerAtomQuantity-inl.h | 801 +
lib/atc/PerAtomQuantity.h | 1469 +
lib/atc/PerAtomQuantityLibrary.cpp | 2383 +
lib/atc/PerAtomQuantityLibrary.h | 1727 +
lib/atc/PerPairQuantity.cpp | 370 +
lib/atc/PerPairQuantity.h | 425 +
lib/atc/PhysicsModel.cpp | 443 +
lib/atc/PhysicsModel.h | 383 +-
lib/atc/PhysicsModelThermal.cpp | 84 -
lib/atc/PhysicsModelThermal.h | 53 -
lib/atc/PhysicsModelTwoTemperature.cpp | 123 -
lib/atc/PhysicsModelTwoTemperature.h | 71 -
lib/atc/PoissonSolver.cpp | 216 +
lib/atc/PoissonSolver.h | 137 +
lib/atc/PolynomialSolver.cpp | 139 +
lib/atc/PolynomialSolver.h | 14 +
lib/atc/PrescribedDataManager.cpp | 219 +-
lib/atc/PrescribedDataManager.h | 302 +-
lib/atc/Quadrature.cpp | 81 +
lib/atc/Quadrature.h | 62 +-
lib/atc/README | 82 +-
lib/atc/SchrodingerSolver.cpp | 559 +
lib/atc/SchrodingerSolver.h | 204 +
lib/atc/ShapeFunction.h | 521 +
lib/atc/Solver.cpp | 147 -
lib/atc/Solver.h | 13 -
lib/atc/SparseMatrix-inl.h | 608 +-
lib/atc/SparseMatrix.h | 167 +-
lib/atc/SparseVector-inl.h | 100 +-
lib/atc/SparseVector.h | 62 +-
lib/atc/SpeciesTimeIntegrator.cpp | 251 +
lib/atc/SpeciesTimeIntegrator.h | 177 +
lib/atc/Stress.cpp | 620 +
lib/atc/Stress.h | 212 +
lib/atc/StringManip.h | 122 -
lib/atc/ThermalTimeIntegrator.cpp | 698 +
lib/atc/ThermalTimeIntegrator.h | 348 +
lib/atc/Thermostat.cpp | 2662 +-
lib/atc/Thermostat.h | 842 +-
lib/atc/TimeFilter.cpp | 645 +-
lib/atc/TimeFilter.h | 193 +-
lib/atc/TimeIntegrator.cpp | 187 +-
lib/atc/TimeIntegrator.h | 218 +-
lib/atc/TransferLibrary.cpp | 2008 +
lib/atc/TransferLibrary.h | 1724 +
lib/atc/TransferOperator.cpp | 911 +
lib/atc/TransferOperator.h | 1145 +
lib/atc/Utility.h | 386 +-
lib/atc/Vector.cpp | 6 +-
lib/atc/Vector.h | 29 +-
lib/atc/ViscousStress.cpp | 82 +
lib/atc/ViscousStress.h | 64 +
lib/atc/VoigtOperations.h | 265 +
lib/atc/WeakEquation.h | 108 +
lib/atc/WeakEquationChargeDiffusion.cpp | 39 +
lib/atc/WeakEquationChargeDiffusion.h | 41 +
lib/atc/WeakEquationDiffusion.cpp | 50 +
lib/atc/WeakEquationDiffusion.h | 50 +
lib/atc/WeakEquationElectronContinuity.cpp | 105 +
lib/atc/WeakEquationElectronContinuity.h | 108 +
lib/atc/WeakEquationElectronMomentum.cpp | 185 +
lib/atc/WeakEquationElectronMomentum.h | 117 +
lib/atc/WeakEquationElectronTemperature.cpp | 227 +
lib/atc/WeakEquationElectronTemperature.h | 180 +
lib/atc/WeakEquationMassDiffusion.cpp | 50 +
lib/atc/WeakEquationMassDiffusion.h | 52 +
lib/atc/WeakEquationMomentum.cpp | 157 +
lib/atc/WeakEquationMomentum.h | 174 +
lib/atc/WeakEquationPhononTemperature.cpp | 124 +
lib/atc/WeakEquationPhononTemperature.h | 116 +
lib/atc/WeakEquationPoisson.cpp | 94 +
lib/atc/WeakEquationPoisson.h | 116 +
lib/atc/WeakEquationSchrodinger.cpp | 47 +
lib/atc/WeakEquationSchrodinger.h | 52 +
lib/atc/XT_Function.cpp | 257 -
lib/atc/XT_Function.h | 172 -
lib/awpmd/Makefile.lammps.empty | 5 +
.../{Makefile.lammps => Makefile.lammps.installed} | 0
lib/awpmd/Makefile.lammps.linalg | 5 +
lib/awpmd/Makefile.mingw32-cross | 80 +
lib/awpmd/Makefile.mingw32-cross-mpi | 13 +
lib/awpmd/Makefile.mingw64-cross | 79 +
lib/awpmd/Makefile.mingw64-cross-mpi | 13 +
lib/awpmd/Makefile.openmpi | 7 +-
lib/awpmd/README | 75 +-
lib/awpmd/ivutils/include/lapack_inter.h | 2 +-
lib/awpmd/ivutils/include/logexc.h | 4 +-
lib/awpmd/ivutils/include/wavepacket.h | 8 +-
lib/colvars/Makefile.fermi | 5 +
lib/colvars/Makefile.g++ | 19 +-
.../{Makefile.lammps => Makefile.lammps.debug} | 0
.../{Makefile.lammps => Makefile.lammps.empty} | 0
lib/colvars/Makefile.mingw32-cross | 111 +
lib/colvars/Makefile.mingw32-cross-mpi | 13 +
lib/colvars/Makefile.mingw64-cross | 109 +
lib/colvars/Makefile.mingw64-cross-mpi | 13 +
lib/colvars/README | 80 +-
lib/colvars/colvar.cpp | 185 +-
lib/colvars/colvar.h | 13 +-
lib/colvars/colvaratoms.cpp | 431 +-
lib/colvars/colvaratoms.h | 98 +-
lib/colvars/colvarbias.cpp | 210 +-
lib/colvars/colvarbias.h | 76 +-
lib/colvars/colvarbias_abf.cpp | 60 +-
lib/colvars/colvarbias_abf.h | 6 +-
lib/colvars/colvarbias_meta.cpp | 180 +-
lib/colvars/colvarbias_meta.h | 14 +-
lib/colvars/colvarcomp.cpp | 82 +-
lib/colvars/colvarcomp.h | 225 +-
lib/colvars/colvarcomp_angles.cpp | 4 +-
lib/colvars/colvarcomp_coordnums.cpp | 67 +-
lib/colvars/colvarcomp_distances.cpp | 734 +-
lib/colvars/colvarcomp_protein.cpp | 16 +-
lib/colvars/colvarcomp_rotations.cpp | 86 +-
lib/colvars/colvargrid.cpp | 4 +-
lib/colvars/colvargrid.h | 55 +-
lib/colvars/colvarmodule.cpp | 254 +-
lib/colvars/colvarmodule.h | 84 +-
lib/colvars/colvarparse.cpp | 47 +-
lib/colvars/colvarparse.h | 10 +-
lib/colvars/colvarproxy.h | 78 +-
lib/colvars/colvartypes.h | 91 +-
lib/colvars/colvarvalue.cpp | 14 +-
lib/colvars/colvarvalue.h | 24 +-
lib/cuda/Makefile.common | 22 +-
lib/cuda/Makefile.defaults | 4 +-
lib/cuda/Makefile.lammps | 9 +-
lib/cuda/README | 77 +-
lib/cuda/atom_vec_angle_cuda.cu | 70 +-
lib/cuda/atom_vec_angle_cuda_cu.h | 18 +-
lib/cuda/atom_vec_atomic_cuda.cu | 70 +-
lib/cuda/atom_vec_atomic_cuda_cu.h | 18 +-
lib/cuda/atom_vec_charge_cuda.cu | 70 +-
lib/cuda/atom_vec_charge_cuda_cu.h | 18 +-
lib/cuda/atom_vec_cuda.cu | 970 +-
lib/cuda/atom_vec_cuda_kernel.cu | 679 +-
lib/cuda/atom_vec_full_cuda.cu | 70 +-
lib/cuda/atom_vec_full_cuda_cu.h | 18 +-
lib/cuda/binning.cu | 196 -
lib/cuda/binning_cu.h | 28 -
lib/cuda/binning_kernel.cu | 149 -
lib/cuda/comm_cuda.cu | 838 +-
lib/cuda/comm_cuda_cu.h | 34 +-
lib/cuda/comm_cuda_kernel.cu | 601 +-
lib/cuda/compute_temp_cuda.cu | 161 +-
lib/cuda/compute_temp_cuda_cu.h | 18 +-
lib/cuda/compute_temp_cuda_kernel.cu | 145 +-
lib/cuda/compute_temp_partial_cuda.cu | 225 +-
lib/cuda/compute_temp_partial_cuda_cu.h | 22 +-
lib/cuda/compute_temp_partial_cuda_kernel.cu | 223 +-
lib/cuda/crm_cuda_utils.cu | 1090 +-
lib/cuda/cuda.cu | 30 +-
lib/cuda/cuda_common.h | 160 +-
lib/cuda/cuda_data.cu | 340 +-
lib/cuda/cuda_data_cu.h | 12 +-
lib/cuda/cuda_data_kernel.cu | 313 +-
lib/cuda/cuda_pair.cu | 1640 +-
lib/cuda/cuda_pair_cu.h | 16 +-
lib/cuda/cuda_pair_kernel.cu | 2622 +-
lib/cuda/cuda_pair_virial_kernel_nc.cu | 204 +-
lib/cuda/cuda_precision.h | 239 +-
lib/cuda/cuda_shared.h | 658 +-
lib/cuda/cuda_wrapper.cu | 416 +-
lib/cuda/cuda_wrapper_cu.h | 28 +-
lib/cuda/cuda_wrapper_kernel.cu | 14 +-
lib/cuda/domain.cu | 298 +-
lib/cuda/domain_cu.h | 20 +-
lib/cuda/domain_kernel.cu | 400 +-
lib/cuda/fft3d_cuda.cu | 106 +-
lib/cuda/fft3d_cuda_cu.h | 22 +-
lib/cuda/fft3d_cuda_kernel.cu | 34 +-
lib/cuda/fix_addforce_cuda.cu | 100 +-
lib/cuda/fix_addforce_cuda_cu.h | 16 +-
lib/cuda/fix_addforce_cuda_kernel.cu | 118 +-
lib/cuda/fix_aveforce_cuda.cu | 123 +-
lib/cuda/fix_aveforce_cuda_cu.h | 18 +-
lib/cuda/fix_aveforce_cuda_kernel.cu | 113 +-
lib/cuda/fix_enforce2d_cuda.cu | 47 +-
lib/cuda/fix_enforce2d_cuda_cu.h | 14 +-
lib/cuda/fix_enforce2d_cuda_kernel.cu | 27 +-
lib/cuda/fix_freeze_cuda.cu | 109 +-
lib/cuda/fix_freeze_cuda_cu.h | 16 +-
lib/cuda/fix_freeze_cuda_kernel.cu | 101 +-
lib/cuda/fix_gravity_cuda.cu | 101 +-
lib/cuda/fix_gravity_cuda_cu.h | 16 +-
lib/cuda/fix_gravity_cuda_kernel.cu | 32 +-
lib/cuda/fix_nh_cuda.cu | 357 +-
lib/cuda/fix_nh_cuda_cu.h | 26 +-
lib/cuda/fix_nh_cuda_kernel.cu | 308 +-
lib/cuda/fix_nve_cuda.cu | 203 +-
lib/cuda/fix_nve_cuda_cu.h | 14 +-
lib/cuda/fix_nve_cuda_kernel.cu | 241 +-
lib/cuda/fix_set_force_cuda.cu | 107 +-
lib/cuda/fix_set_force_cuda_cu.h | 16 +-
lib/cuda/fix_set_force_cuda_kernel.cu | 101 +-
lib/cuda/fix_shake_cuda.cu | 420 +-
lib/cuda/fix_shake_cuda_cu.h | 30 +-
lib/cuda/fix_shake_cuda_kernel.cu | 1261 +-
lib/cuda/fix_temp_berendsen_cuda.cu | 56 +-
lib/cuda/fix_temp_berendsen_cuda_cu.h | 16 +-
lib/cuda/fix_temp_berendsen_cuda_kernel.cu | 29 +-
lib/cuda/fix_temp_rescale_cuda.cu | 54 +-
lib/cuda/fix_temp_rescale_cuda_cu.h | 16 +-
lib/cuda/fix_temp_rescale_cuda_kernel.cu | 29 +-
lib/cuda/fix_temp_rescale_limit_cuda.cu | 54 +-
lib/cuda/fix_temp_rescale_limit_cuda_cu.h | 16 +-
lib/cuda/fix_temp_rescale_limit_cuda_kernel.cu | 43 +-
lib/cuda/fix_viscous_cuda.cu | 61 +-
lib/cuda/fix_viscous_cuda_cu.h | 16 +-
lib/cuda/fix_viscous_cuda_kernel.cu | 30 +-
lib/cuda/neighbor.cu | 611 +-
lib/cuda/neighbor_cu.h | 14 +-
lib/cuda/neighbor_kernel.cu | 1146 +-
lib/cuda/pair_born_coul_long_cuda.cu | 68 +-
lib/cuda/pair_born_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_born_coul_long_cuda_kernel_nc.cu | 36 +-
lib/cuda/pair_buck_coul_cut_cuda.cu | 67 +-
lib/cuda/pair_buck_coul_cut_cuda_cu.h | 16 +-
lib/cuda/pair_buck_coul_long_cuda.cu | 67 +-
lib/cuda/pair_buck_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_buck_cuda.cu | 67 +-
lib/cuda/pair_buck_cuda_cu.h | 16 +-
lib/cuda/pair_buck_cuda_kernel_nc.cu | 34 +-
lib/cuda/pair_cg_cmm_coul_cut_cuda.cu | 67 +-
lib/cuda/pair_cg_cmm_coul_cut_cuda_cu.h | 16 +-
lib/cuda/pair_cg_cmm_coul_debye_cuda.cu | 67 +-
lib/cuda/pair_cg_cmm_coul_debye_cuda_cu.h | 16 +-
lib/cuda/pair_cg_cmm_coul_long_cuda.cu | 67 +-
lib/cuda/pair_cg_cmm_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_cg_cmm_cuda.cu | 76 +-
lib/cuda/pair_cg_cmm_cuda_cu.h | 16 +-
lib/cuda/pair_cg_cmm_cuda_kernel_nc.cu | 41 +-
lib/cuda/pair_eam_cuda.cu | 425 +-
lib/cuda/pair_eam_cuda_cu.h | 28 +-
lib/cuda/pair_eam_cuda_kernel_nc.cu | 593 +-
lib/cuda/pair_gran_hooke_cuda.cu | 285 +-
lib/cuda/pair_gran_hooke_cuda_cu.h | 16 +-
lib/cuda/pair_gran_hooke_cuda_kernel_nc.cu | 410 +-
lib/cuda/pair_lj96_cut_cuda.cu | 65 +-
lib/cuda/pair_lj96_cut_cuda_cu.h | 16 +-
lib/cuda/pair_lj96_cut_cuda_kernel_nc.cu | 30 +-
lib/cuda/pair_lj_charmm_coul_charmm_cuda.cu | 73 +-
lib/cuda/pair_lj_charmm_coul_charmm_cuda_cu.h | 16 +-
.../pair_lj_charmm_coul_charmm_cuda_kernel_nc.cu | 103 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda.cu | 73 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda_cu.h | 16 +-
...j_charmm_coul_charmm_implicit_cuda_kernel_nc.cu | 48 +-
lib/cuda/pair_lj_charmm_coul_long_cuda.cu | 69 +-
lib/cuda/pair_lj_charmm_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_lj_class2_coul_cut_cuda.cu | 67 +-
lib/cuda/pair_lj_class2_coul_cut_cuda_cu.h | 16 +-
lib/cuda/pair_lj_class2_coul_long_cuda.cu | 67 +-
lib/cuda/pair_lj_class2_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_lj_class2_cuda.cu | 69 +-
lib/cuda/pair_lj_class2_cuda_cu.h | 16 +-
lib/cuda/pair_lj_class2_cuda_kernel_nc.cu | 30 +-
lib/cuda/pair_lj_cut_coul_cut_cuda.cu | 67 +-
lib/cuda/pair_lj_cut_coul_cut_cuda_cu.h | 16 +-
lib/cuda/pair_lj_cut_coul_debye_cuda.cu | 67 +-
lib/cuda/pair_lj_cut_coul_debye_cuda_cu.h | 16 +-
lib/cuda/pair_lj_cut_coul_long_cuda.cu | 67 +-
lib/cuda/pair_lj_cut_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_lj_cut_cuda.cu | 69 +-
lib/cuda/pair_lj_cut_cuda_cu.h | 16 +-
lib/cuda/pair_lj_cut_cuda_kernel_nc.cu | 28 +-
lib/cuda/pair_lj_cut_experimental_cuda.cu | 75 +-
lib/cuda/pair_lj_cut_experimental_cuda_cu.h | 16 +-
lib/cuda/pair_lj_expand_cuda.cu | 65 +-
lib/cuda/pair_lj_expand_cuda_cu.h | 16 +-
lib/cuda/pair_lj_expand_cuda_kernel_nc.cu | 34 +-
lib/cuda/pair_lj_gromacs_coul_gromacs_cuda.cu | 83 +-
lib/cuda/pair_lj_gromacs_coul_gromacs_cuda_cu.h | 16 +-
.../pair_lj_gromacs_coul_gromacs_cuda_kernel_nc.cu | 61 +-
lib/cuda/pair_lj_gromacs_cuda.cu | 61 +-
lib/cuda/pair_lj_gromacs_cuda_cu.h | 16 +-
lib/cuda/pair_lj_gromacs_cuda_kernel_nc.cu | 63 +-
lib/cuda/pair_lj_sdk_coul_cut_cuda.cu | 67 +-
lib/cuda/pair_lj_sdk_coul_cut_cuda_cu.h | 16 +-
lib/cuda/pair_lj_sdk_coul_debye_cuda.cu | 67 +-
lib/cuda/pair_lj_sdk_coul_debye_cuda_cu.h | 16 +-
lib/cuda/pair_lj_sdk_coul_long_cuda.cu | 67 +-
lib/cuda/pair_lj_sdk_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_lj_sdk_cuda.cu | 76 +-
lib/cuda/pair_lj_sdk_cuda_cu.h | 16 +-
lib/cuda/pair_lj_sdk_cuda_kernel_nc.cu | 41 +-
lib/cuda/pair_lj_smooth_cuda.cu | 63 +-
lib/cuda/pair_lj_smooth_cuda_cu.h | 16 +-
lib/cuda/pair_lj_smooth_cuda_kernel_nc.cu | 89 +-
lib/cuda/pair_manybody_const.h | 4 +-
lib/cuda/pair_morse_coul_long_cuda.cu | 68 +-
lib/cuda/pair_morse_coul_long_cuda_cu.h | 16 +-
lib/cuda/pair_morse_coul_long_cuda_kernel_nc.cu | 34 +-
lib/cuda/pair_morse_cuda.cu | 65 +-
lib/cuda/pair_morse_cuda_cu.h | 16 +-
lib/cuda/pair_morse_cuda_kernel_nc.cu | 28 +-
lib/cuda/pair_sw_cuda.cu | 157 +-
lib/cuda/pair_sw_cuda_cu.h | 42 +-
lib/cuda/pair_sw_cuda_kernel_nc.cu | 521 +-
lib/cuda/pair_tersoff_cuda.cu | 173 +-
lib/cuda/pair_tersoff_cuda_cu.h | 48 +-
lib/cuda/pair_tersoff_cuda_kernel_nc.cu | 1202 +-
lib/cuda/pair_virial_compute_cu.h | 14 +-
lib/cuda/pppm_cuda.cu | 771 +-
lib/cuda/pppm_cuda_cu.h | 62 +-
lib/cuda/pppm_cuda_kernel.cu | 1228 +-
lib/gpu/Makefile.lammps.mac_ocl | 5 +
lib/gpu/Makefile.lammps.mingw-cross | 6 +
lib/gpu/Makefile.lammps.opencl | 5 +
.../{Makefile.lammps => Makefile.lammps.standard} | 0
lib/gpu/Makefile.lens | 5 +
lib/gpu/Makefile.lincoln | 4 +
lib/gpu/Makefile.linux | 4 +
lib/gpu/Makefile.linux.double | 37 +
lib/gpu/Makefile.linux.mixed | 37 +
lib/gpu/Makefile.linux_opencl | 11 +-
lib/gpu/Makefile.longhorn | 4 +
lib/gpu/Makefile.mac | 4 +
lib/gpu/Makefile.mac_opencl | 9 +
lib/gpu/Makefile.mingw32-cross | 17 +
lib/gpu/Makefile.mingw32-cross-mpi | 19 +
lib/gpu/Makefile.mingw64-cross | 18 +
lib/gpu/Makefile.mingw64-cross-mpi | 20 +
lib/gpu/Makefile.serial | 4 +
lib/gpu/Makefile.serial_opencl | 5 +
lib/gpu/Makefile.xk7 | 32 +
lib/gpu/Nvidia.makefile | 599 +-
lib/gpu/Opencl.makefile | 205 +-
lib/gpu/README | 111 +-
lib/gpu/geryon/README | 4 +
lib/gpu/geryon/VERSION.txt | 2 +-
lib/gpu/geryon/nvc_device.h | 346 -
lib/gpu/geryon/nvc_macros.h | 78 -
lib/gpu/geryon/nvc_texture.h | 69 -
lib/gpu/geryon/nvd_device.h | 95 +-
lib/gpu/geryon/nvd_kernel.h | 184 +-
lib/gpu/geryon/nvd_mat.h | 3 +
lib/gpu/geryon/nvd_memory.h | 75 +-
lib/gpu/geryon/nvd_texture.h | 47 +-
lib/gpu/geryon/ocl_device.h | 214 +-
lib/gpu/geryon/ocl_kernel.h | 154 +-
lib/gpu/geryon/ocl_mat.h | 3 +
lib/gpu/geryon/ocl_memory.h | 346 +-
lib/gpu/geryon/ocl_timer.h | 12 +-
lib/gpu/geryon/ucl_arg_kludge.h | 438 -
lib/gpu/geryon/ucl_basemat.h | 27 +-
lib/gpu/geryon/ucl_copy.h | 214 +-
lib/gpu/geryon/ucl_d_mat.h | 106 +-
lib/gpu/geryon/ucl_d_vec.h | 104 +-
lib/gpu/geryon/ucl_h_mat.h | 103 +-
lib/gpu/geryon/ucl_h_vec.h | 97 +-
lib/gpu/geryon/ucl_matrix.h | 239 +
lib/gpu/geryon/ucl_print.h | 9 +
lib/gpu/geryon/ucl_s_obj_help.h | 397 +
lib/gpu/geryon/ucl_types.h | 61 +-
lib/gpu/geryon/ucl_vector.h | 238 +
lib/gpu/lal_answer.cpp | 305 +-
lib/gpu/lal_answer.h | 35 +-
lib/gpu/lal_atom.cpp | 204 +-
lib/gpu/lal_atom.cu | 6 +-
lib/gpu/lal_atom.h | 125 +-
lib/gpu/lal_aux_fun1.h | 81 +-
lib/gpu/lal_base_atomic.cpp | 28 +-
lib/gpu/lal_base_atomic.h | 11 +-
lib/gpu/lal_base_charge.cpp | 30 +-
lib/gpu/lal_base_charge.h | 13 +-
lib/gpu/lal_base_dipole.cpp | 311 +
lib/gpu/lal_base_dipole.h | 200 +
lib/gpu/lal_base_ellipsoid.cpp | 76 +-
lib/gpu/lal_base_ellipsoid.h | 27 +-
lib/gpu/lal_base_three.cpp | 358 +
lib/gpu/lal_base_three.h | 221 +
lib/gpu/lal_beck.cpp | 152 +
lib/gpu/lal_beck.cu | 225 +
lib/gpu/lal_beck.h | 80 +
lib/gpu/lal_beck_ext.cpp | 120 +
lib/gpu/lal_born.cpp | 162 +
lib/gpu/lal_born.cu | 210 +
lib/gpu/lal_born.h | 84 +
lib/gpu/lal_born_coul_long.cpp | 175 +
lib/gpu/lal_born_coul_long.cu | 273 +
lib/gpu/lal_born_coul_long.h | 88 +
lib/gpu/lal_born_coul_long_ext.cpp | 132 +
lib/gpu/lal_born_coul_wolf.cpp | 176 +
lib/gpu/lal_born_coul_wolf.cu | 295 +
lib/gpu/lal_born_coul_wolf.h | 89 +
lib/gpu/lal_born_coul_wolf_ext.cpp | 134 +
lib/gpu/lal_born_ext.cpp | 124 +
lib/gpu/lal_buck.cpp | 31 +-
lib/gpu/lal_buck.cu | 61 +-
lib/gpu/lal_buck_coul.cpp | 35 +-
lib/gpu/lal_buck_coul.cu | 93 +-
lib/gpu/lal_buck_coul_long.cpp | 36 +-
lib/gpu/lal_buck_coul_long.cu | 92 +-
lib/gpu/lal_cg_cmm.cpp | 30 +-
lib/gpu/lal_cg_cmm.cu | 61 +-
lib/gpu/lal_cg_cmm_long.cpp | 37 +-
lib/gpu/lal_cg_cmm_long.cu | 87 +-
lib/gpu/lal_charmm_long.cpp | 29 +-
lib/gpu/lal_charmm_long.cu | 96 +-
lib/gpu/lal_colloid.cpp | 181 +
lib/gpu/lal_colloid.cu | 343 +
lib/gpu/lal_colloid.h | 89 +
lib/gpu/lal_colloid_ext.cpp | 127 +
lib/gpu/lal_coul_dsf.cpp | 153 +
lib/gpu/lal_coul_dsf.cu | 236 +
lib/gpu/lal_coul_dsf.h | 78 +
lib/gpu/lal_coul_dsf_ext.cpp | 125 +
lib/gpu/lal_coul_long.cpp | 32 +-
lib/gpu/lal_coul_long.cu | 321 +-
lib/gpu/lal_device.cpp | 153 +-
lib/gpu/lal_device.cu | 4 +-
lib/gpu/lal_device.h | 24 +-
lib/gpu/lal_dipole_lj.cpp | 170 +
lib/gpu/lal_dipole_lj.cu | 555 +
lib/gpu/lal_dipole_lj.h | 85 +
lib/gpu/lal_dipole_lj_ext.cpp | 128 +
lib/gpu/lal_dipole_lj_sf.cpp | 170 +
lib/gpu/lal_dipole_lj_sf.cu | 618 +
lib/gpu/lal_dipole_lj_sf.h | 85 +
lib/gpu/lal_dipole_lj_sf_ext.cpp | 128 +
lib/gpu/lal_eam.cpp | 139 +-
lib/gpu/lal_eam.cu | 325 +-
lib/gpu/lal_eam.h | 17 +-
lib/gpu/lal_eam_ext.cpp | 14 +-
lib/gpu/lal_ellipsoid_extra.h | 149 +-
lib/gpu/lal_ellipsoid_nbor.cu | 45 +-
lib/gpu/lal_gauss.cpp | 146 +
lib/gpu/lal_gauss.cu | 197 +
lib/gpu/lal_gauss.h | 77 +
lib/gpu/lal_gauss_ext.cpp | 120 +
lib/gpu/lal_gayberne.cpp | 89 +-
lib/gpu/lal_gayberne.cu | 36 +-
lib/gpu/lal_gayberne_lj.cu | 92 +-
lib/gpu/lal_lj.cpp | 31 +-
lib/gpu/lal_lj.cu | 61 +-
lib/gpu/lal_lj96.cpp | 30 +-
lib/gpu/lal_lj96.cu | 61 +-
lib/gpu/lal_lj_class2_long.cpp | 31 +-
lib/gpu/lal_lj_class2_long.cu | 89 +-
lib/gpu/lal_lj_coul.cpp | 35 +-
lib/gpu/lal_lj_coul.cu | 95 +-
lib/gpu/lal_lj_coul_debye.cpp | 168 +
lib/gpu/lal_lj_coul_debye.cu | 267 +
lib/gpu/lal_lj_coul_debye.h | 85 +
lib/gpu/lal_lj_coul_debye_ext.cpp | 129 +
lib/gpu/lal_lj_coul_long.cpp | 31 +-
lib/gpu/lal_lj_coul_long.cu | 87 +-
lib/gpu/lal_lj_coul_msm.cpp | 200 +
lib/gpu/lal_lj_coul_msm.cu | 322 +
lib/gpu/lal_lj_coul_msm.h | 88 +
lib/gpu/lal_lj_coul_msm_ext.cpp | 131 +
lib/gpu/lal_lj_dsf.cpp | 168 +
lib/gpu/lal_lj_dsf.cu | 285 +
lib/gpu/lal_lj_dsf.h | 85 +
lib/gpu/lal_lj_dsf_ext.cpp | 132 +
lib/gpu/lal_lj_expand.cpp | 31 +-
lib/gpu/lal_lj_expand.cu | 57 +-
lib/gpu/lal_mie.cpp | 152 +
lib/gpu/lal_mie.cu | 203 +
lib/gpu/lal_mie.h | 80 +
lib/gpu/lal_mie_ext.cpp | 124 +
lib/gpu/lal_morse.cpp | 31 +-
lib/gpu/lal_morse.cu | 63 +-
lib/gpu/lal_neighbor.cpp | 288 +-
lib/gpu/lal_neighbor.h | 51 +-
lib/gpu/lal_neighbor_cpu.cu | 7 +-
lib/gpu/lal_neighbor_gpu.cu | 93 +-
lib/gpu/lal_neighbor_shared.cpp | 18 +-
lib/gpu/lal_neighbor_shared.h | 13 +-
lib/gpu/lal_pppm.cpp | 91 +-
lib/gpu/lal_pppm.cu | 52 +-
lib/gpu/lal_pppm.h | 15 +-
lib/gpu/lal_pppm_ext.cpp | 9 +-
lib/gpu/lal_precision.h | 23 +-
lib/gpu/lal_preprocessor.h | 166 +-
lib/gpu/lal_re_squared.cpp | 102 +-
lib/gpu/lal_re_squared.cu | 33 +-
lib/gpu/lal_re_squared_lj.cu | 303 +-
lib/gpu/lal_soft.cpp | 145 +
lib/gpu/lal_soft.cu | 201 +
lib/gpu/lal_soft.h | 77 +
lib/gpu/lal_soft_ext.cpp | 120 +
lib/gpu/lal_sw.cpp | 167 +
lib/gpu/lal_sw.cu | 622 +
lib/gpu/lal_sw.h | 73 +
lib/gpu/lal_sw_ext.cpp | 128 +
lib/gpu/lal_table.cpp | 141 +-
lib/gpu/lal_table.cu | 294 +-
lib/gpu/lal_yukawa.cpp | 31 +-
lib/gpu/lal_yukawa.cu | 71 +-
lib/gpu/lal_yukawa_colloid.cpp | 291 +
lib/gpu/lal_yukawa_colloid.cu | 212 +
lib/gpu/lal_yukawa_colloid.h | 122 +
lib/gpu/lal_yukawa_colloid_ext.cpp | 123 +
lib/linalg/Makefile.gfortran | 24 +-
lib/linalg/Makefile.mingw32-cross | 85 +
lib/linalg/Makefile.mingw32-cross-mpi | 13 +
lib/linalg/Makefile.mingw64-cross | 85 +
lib/linalg/Makefile.mingw64-cross-mpi | 13 +
lib/linalg/Makefile.mingw_cross | 63 -
lib/linalg/README | 29 +-
lib/linalg/dasum.f | 119 +-
lib/linalg/daxpy.f | 126 +-
lib/linalg/dcopy.f | 133 +-
lib/linalg/ddot.f | 127 +-
lib/linalg/dgecon.f | 179 +-
lib/linalg/dgemm.f | 320 +-
lib/linalg/dgemv.f | 256 +-
lib/linalg/dger.f | 207 +-
lib/linalg/dgetf2.f | 155 +-
lib/linalg/dgetrf.f | 155 +-
lib/linalg/dgetri.f | 164 +-
lib/linalg/disnan.f | 80 +
lib/linalg/dlabad.f | 103 +-
lib/linalg/dlacn2.f | 197 +-
lib/linalg/dlaisnan.f | 91 +
lib/linalg/dlange.f | 184 +-
lib/linalg/dlassq.f | 156 +-
lib/linalg/dlaswp.f | 161 +-
lib/linalg/dlatrs.f | 399 +-
lib/linalg/drscl.f | 113 +-
lib/linalg/dscal.f | 120 +-
lib/linalg/dswap.f | 145 +-
lib/linalg/dtrmm.f | 304 +-
lib/linalg/dtrmv.f | 247 +-
lib/linalg/dtrsm.f | 311 +-
lib/linalg/dtrsv.f | 244 +-
lib/linalg/dtrti2.f | 159 +-
lib/linalg/dtrtri.f | 157 +-
lib/linalg/idamax.f | 110 +-
lib/linalg/ieeeck.f | 117 +-
lib/linalg/ilaenv.f | 259 +-
lib/linalg/iparmq.f | 368 +-
lib/linalg/lsame.f | 123 +-
lib/linalg/xerbla.f | 95 +-
lib/linalg/zdotc.f | 101 +
lib/linalg/zdscal.f | 94 +
lib/linalg/zhpr.f | 279 +
lib/linalg/zpptrf.f | 241 +
lib/linalg/zpptri.f | 190 +
lib/linalg/zscal.f | 91 +
lib/linalg/ztpmv.f | 388 +
lib/linalg/ztpsv.f | 390 +
lib/linalg/ztptri.f | 242 +
lib/meam/Makefile.g95 | 7 +-
lib/meam/Makefile.gfortran | 13 +-
lib/meam/Makefile.ifort | 7 +-
lib/meam/Makefile.lammps | 5 -
lib/meam/Makefile.mingw32-cross | 65 +
lib/meam/Makefile.mingw32-cross-mpi | 13 +
lib/meam/Makefile.mingw64-cross | 65 +
lib/meam/Makefile.mingw64-cross-mpi | 13 +
lib/meam/Makefile.pgf90 | 7 +-
lib/meam/Makefile.tbird | 16 +-
lib/meam/README | 66 +-
lib/meam/meam_setup_param.F | 44 +
lib/poems/Makefile.g++ | 8 +-
lib/poems/Makefile.icc | 8 +-
.../{Makefile.lammps => Makefile.lammps.empty} | 0
lib/poems/Makefile.mingw32-cross | 113 +
lib/poems/Makefile.mingw32-cross-mpi | 13 +
lib/poems/Makefile.mingw64-cross | 113 +
lib/poems/Makefile.mingw64-cross-mpi | 13 +
lib/poems/Makefile.storm | 101 -
lib/poems/README | 69 +-
lib/reax/Makefile.g77 | 61 -
lib/reax/Makefile.g95 | 20 +-
lib/reax/Makefile.gfortran | 26 +-
lib/reax/Makefile.ifort | 26 +-
lib/reax/Makefile.lammps | 5 -
lib/reax/Makefile.pgf90 | 20 +-
lib/reax/Makefile.redsky | 27 +-
lib/reax/Makefile.tbird | 26 +-
lib/reax/README | 123 +-
potentials/BNC.tersoff | 73 +
potentials/CdTe.sw | 68 +-
potentials/MOH.nb3b.harmonic | 20 +
potentials/README | 12 +
potentials/README.reax | 9 +-
potentials/Si.b.meam.sw.spline | 133 +
potentials/Si.tersoff.mod | 25 +
potentials/Ti.meam.sw.spline | 72 +
potentials/ffield.comb3 | 349 +
potentials/ffield.reax.Al_Al0_AlN | 274 -
potentials/ffield.reax.FC | 361 +
potentials/ffield.reax.ZnOH | 2 +-
potentials/ffield.reax.budzien | 2 +-
potentials/ffield.reax.lg | 2 +-
potentials/ffield.reax.mattsson | 2 +-
potentials/lib.comb3 | 24303 +++++
python/README | 43 +-
python/examples/demo.py | 21 +-
python/examples/gui.py | 2 +-
python/examples/plot.py | 2 +-
python/examples/simple.py | 8 +-
python/examples/trivial.py | 2 +-
python/examples/viz_atomeye.py | 2 +-
python/examples/viz_gl.py | 2 +-
python/examples/viz_pymol.py | 2 +-
python/examples/viz_vmd.py | 2 +-
python/examples/vizplotgui_atomeye.py | 2 +-
python/examples/vizplotgui_gl.py | 2 +-
python/examples/vizplotgui_pymol.py | 2 +-
python/examples/vizplotgui_vmd.py | 2 +-
python/install.py | 67 +
python/lammps.py | 108 +-
python/setup.py | 39 -
python/setup_serial.py | 34 -
regress/benchmark.py | 235 +
regress/melt/in.melt | 20 +
regress/melt/log.melt.linux.4 | 60 +
regress/min/in.min | 26 +
regress/min/in.min.box | 31 +
regress/min/log.min.box.linux.4 | 335 +
regress/min/log.min.linux.4 | 97 +
regress/regression.sh | 14 +
src/ASPHERE/Install.sh | 67 -
src/ASPHERE/compute_erotate_asphere.cpp | 96 +-
src/ASPHERE/compute_erotate_asphere.h | 2 +-
src/ASPHERE/compute_temp_asphere.cpp | 234 +-
src/ASPHERE/compute_temp_asphere.h | 3 +-
src/ASPHERE/fix_nh_asphere.cpp | 17 +-
src/ASPHERE/fix_nh_asphere.h | 2 +-
src/ASPHERE/fix_nph_asphere.cpp | 6 +-
src/ASPHERE/fix_nph_asphere.h | 2 +-
src/ASPHERE/fix_npt_asphere.cpp | 6 +-
src/ASPHERE/fix_npt_asphere.h | 2 +-
src/ASPHERE/fix_nve_asphere.cpp | 21 +-
src/ASPHERE/fix_nve_asphere.h | 2 +-
src/ASPHERE/fix_nve_asphere_noforce.cpp | 22 +-
src/ASPHERE/fix_nve_asphere_noforce.h | 4 +-
src/ASPHERE/fix_nve_line.cpp | 14 +-
src/ASPHERE/fix_nve_line.h | 2 +-
src/ASPHERE/fix_nve_tri.cpp | 20 +-
src/ASPHERE/fix_nve_tri.h | 2 +-
src/ASPHERE/fix_nvt_asphere.cpp | 4 +-
src/ASPHERE/fix_nvt_asphere.h | 2 +-
src/ASPHERE/pair_gayberne.cpp | 345 +-
src/ASPHERE/pair_gayberne.h | 20 +-
src/ASPHERE/pair_line_lj.cpp | 347 +-
src/ASPHERE/pair_line_lj.h | 11 +-
src/ASPHERE/pair_resquared.cpp | 92 +-
src/ASPHERE/pair_resquared.h | 18 +-
src/ASPHERE/pair_tri_lj.cpp | 507 +-
src/ASPHERE/pair_tri_lj.h | 11 +-
src/BODY/body_nparticle.cpp | 222 +
src/BODY/body_nparticle.h | 76 +
src/BODY/compute_body_local.cpp | 227 +
src/BODY/compute_body_local.h | 75 +
src/BODY/fix_nve_body.cpp | 132 +
src/BODY/fix_nve_body.h | 53 +
src/BODY/pair_body.cpp | 484 +
src/BODY/pair_body.h | 82 +
src/CLASS2/Install.sh | 43 -
src/CLASS2/angle_class2.cpp | 71 +-
src/CLASS2/angle_class2.h | 3 +-
src/CLASS2/bond_class2.cpp | 34 +-
src/CLASS2/bond_class2.h | 5 +-
src/CLASS2/dihedral_class2.cpp | 277 +-
src/CLASS2/dihedral_class2.h | 5 +-
src/CLASS2/improper_class2.cpp | 403 +-
src/CLASS2/improper_class2.h | 5 +-
src/CLASS2/pair_lj_class2.cpp | 134 +-
src/CLASS2/pair_lj_class2.h | 6 +-
src/CLASS2/pair_lj_class2_coul_cut.cpp | 177 +-
src/CLASS2/pair_lj_class2_coul_cut.h | 6 +-
src/CLASS2/pair_lj_class2_coul_long.cpp | 264 +-
src/CLASS2/pair_lj_class2_coul_long.h | 11 +-
src/COLLOID/Install.sh | 24 -
src/COLLOID/fix_wall_colloid.cpp | 28 +-
src/COLLOID/fix_wall_colloid.h | 2 +-
src/COLLOID/pair_colloid.cpp | 267 +-
src/COLLOID/pair_colloid.h | 8 +-
src/COLLOID/pair_yukawa_colloid.cpp | 73 +-
src/COLLOID/pair_yukawa_colloid.h | 2 +-
src/DIPOLE/Install.sh | 19 -
src/DIPOLE/atom_vec_dipole.cpp | 324 +-
src/DIPOLE/atom_vec_dipole.h | 13 +-
src/DIPOLE/pair_dipole_cut.cpp | 481 -
src/DIPOLE/pair_dipole_cut.h | 70 -
src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 486 +
src/DIPOLE/pair_lj_cut_dipole_cut.h | 74 +
src/DIPOLE/pair_lj_cut_dipole_long.cpp | 560 +
src/DIPOLE/pair_lj_cut_dipole_long.h | 88 +
src/DIPOLE/pair_lj_long_dipole_long.cpp | 683 +
src/DIPOLE/pair_lj_long_dipole_long.h | 134 +
src/Depend.sh | 133 +-
src/FLD/Install.sh | 35 -
src/FLD/pair_brownian.cpp | 344 +-
src/FLD/pair_brownian.h | 20 +-
src/FLD/pair_brownian_poly.cpp | 241 +-
src/FLD/pair_brownian_poly.h | 8 +-
src/FLD/pair_lubricate.cpp | 326 +-
src/FLD/pair_lubricate.h | 18 +-
src/FLD/pair_lubricateU.cpp | 1171 +-
src/FLD/pair_lubricateU.h | 16 +-
src/FLD/pair_lubricateU_poly.cpp | 933 +-
src/FLD/pair_lubricateU_poly.h | 14 +-
src/FLD/pair_lubricate_poly.cpp | 284 +-
src/FLD/pair_lubricate_poly.h | 10 +-
src/GPU/Install.sh | 262 +-
src/GPU/Package.sh | 44 -
src/GPU/fix_gpu.cpp | 121 +-
src/GPU/fix_gpu.h | 9 +-
src/GPU/gpu_extra.h | 53 +-
src/GPU/pair_beck_gpu.cpp | 244 +
src/GPU/pair_beck_gpu.h | 59 +
src/GPU/pair_born_coul_long_gpu.cpp | 298 +
src/GPU/pair_born_coul_long_gpu.h | 68 +
src/GPU/pair_born_coul_wolf_gpu.cpp | 292 +
src/GPU/pair_born_coul_wolf_gpu.h | 59 +
src/GPU/pair_born_gpu.cpp | 233 +
src/GPU/pair_born_gpu.h | 59 +
src/GPU/pair_buck_coul_cut_gpu.cpp | 158 +-
src/GPU/pair_buck_coul_cut_gpu.h | 2 +-
src/GPU/pair_buck_coul_long_gpu.cpp | 170 +-
src/GPU/pair_buck_coul_long_gpu.h | 2 +-
src/GPU/pair_buck_gpu.cpp | 106 +-
src/GPU/pair_buck_gpu.h | 2 +-
src/GPU/pair_colloid_gpu.cpp | 307 +
src/GPU/pair_colloid_gpu.h | 67 +
src/GPU/pair_coul_dsf_gpu.cpp | 272 +
src/GPU/pair_coul_dsf_gpu.h | 63 +
src/GPU/pair_coul_long_gpu.cpp | 164 +-
src/GPU/pair_coul_long_gpu.h | 2 +-
src/GPU/pair_eam_alloy_gpu.cpp | 25 +-
src/GPU/pair_eam_alloy_gpu.h | 2 +-
src/GPU/pair_eam_fs_gpu.cpp | 29 +-
src/GPU/pair_eam_fs_gpu.h | 2 +-
src/GPU/pair_eam_gpu.cpp | 139 +-
src/GPU/pair_eam_gpu.h | 5 +-
src/GPU/pair_gauss_gpu.cpp | 226 +
src/GPU/pair_gauss_gpu.h | 59 +
src/GPU/pair_gayberne_gpu.cpp | 176 +-
src/GPU/pair_gayberne_gpu.h | 10 +-
src/GPU/pair_lj96_cut_gpu.cpp | 98 +-
src/GPU/pair_lj96_cut_gpu.h | 2 +-
src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 244 +-
src/GPU/pair_lj_charmm_coul_long_gpu.h | 2 +-
src/GPU/pair_lj_class2_coul_long_gpu.cpp | 156 +-
src/GPU/pair_lj_class2_coul_long_gpu.h | 2 +-
src/GPU/pair_lj_class2_gpu.cpp | 98 +-
src/GPU/pair_lj_class2_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 128 +-
src/GPU/pair_lj_cut_coul_cut_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 266 +
src/GPU/pair_lj_cut_coul_debye_gpu.h | 63 +
src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 290 +
src/GPU/pair_lj_cut_coul_dsf_gpu.h | 63 +
src/GPU/pair_lj_cut_coul_long_gpu.cpp | 194 +-
src/GPU/pair_lj_cut_coul_long_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 294 +
src/GPU/pair_lj_cut_coul_msm_gpu.h | 59 +
src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 370 +
src/GPU/pair_lj_cut_dipole_cut_gpu.h | 67 +
src/GPU/pair_lj_cut_gpu.cpp | 100 +-
src/GPU/pair_lj_cut_gpu.h | 2 +-
src/GPU/pair_lj_expand_gpu.cpp | 106 +-
src/GPU/pair_lj_expand_gpu.h | 2 +-
src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 196 +-
src/GPU/pair_lj_sdk_coul_long_gpu.h | 2 +-
src/GPU/pair_lj_sdk_gpu.cpp | 144 +-
src/GPU/pair_lj_sdk_gpu.h | 2 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 400 +
src/GPU/pair_lj_sf_dipole_sf_gpu.h | 67 +
src/GPU/pair_mie_cut_gpu.cpp | 230 +
src/GPU/pair_mie_cut_gpu.h | 59 +
src/GPU/pair_morse_gpu.cpp | 100 +-
src/GPU/pair_morse_gpu.h | 2 +-
src/GPU/pair_resquared_gpu.cpp | 72 +-
src/GPU/pair_resquared_gpu.h | 2 +-
src/GPU/pair_soft_gpu.cpp | 225 +
src/GPU/pair_soft_gpu.h | 59 +
src/GPU/pair_sw_gpu.cpp | 178 +
src/GPU/pair_sw_gpu.h | 67 +
src/GPU/pair_table_gpu.cpp | 200 +-
src/GPU/pair_table_gpu.h | 2 +-
src/GPU/pair_yukawa_colloid_gpu.cpp | 241 +
src/GPU/pair_yukawa_colloid_gpu.h | 63 +
src/GPU/pair_yukawa_gpu.cpp | 98 +-
src/GPU/pair_yukawa_gpu.h | 2 +-
src/GPU/pppm_gpu.cpp | 892 +-
src/GPU/pppm_gpu.h | 38 +-
src/Install.sh | 33 +
src/KIM/Install.sh | 44 +-
src/KIM/Makefile.lammps | 25 +
src/KIM/pair_kim.cpp | 1776 +-
src/KIM/pair_kim.h | 248 +-
src/KSPACE/Install.sh | 69 -
src/KSPACE/commgrid.cpp | 571 +
src/KSPACE/commgrid.h | 87 +
src/KSPACE/ewald.cpp | 1248 +-
src/KSPACE/ewald.h | 44 +-
src/KSPACE/ewald_disp.cpp | 1453 +
src/KSPACE/ewald_disp.h | 165 +
src/KSPACE/fft3d.cpp | 216 +-
src/KSPACE/fft3d.h | 72 +-
src/KSPACE/fft3d_wrap.cpp | 18 +-
src/KSPACE/fft3d_wrap.h | 8 +-
src/KSPACE/fix_tune_kspace.cpp | 543 +
src/KSPACE/fix_tune_kspace.h | 109 +
src/KSPACE/kissfft.h | 62 +-
src/KSPACE/msm.cpp | 3400 +
src/KSPACE/msm.h | 236 +
src/KSPACE/msm_cg.cpp | 533 +
src/KSPACE/msm_cg.h | 75 +
src/KSPACE/pair_born_coul_long.cpp | 315 +-
src/KSPACE/pair_born_coul_long.h | 14 +-
src/KSPACE/pair_born_coul_msm.cpp | 198 +
src/KSPACE/pair_born_coul_msm.h | 68 +
src/KSPACE/pair_buck_coul_long.cpp | 264 +-
src/KSPACE/pair_buck_coul_long.h | 17 +-
src/KSPACE/pair_buck_coul_msm.cpp | 193 +
src/KSPACE/pair_buck_coul_msm.h | 68 +
src/KSPACE/pair_buck_long_coul_long.cpp | 1053 +
src/KSPACE/pair_buck_long_coul_long.h | 127 +
src/KSPACE/pair_coul_long.cpp | 325 +-
src/KSPACE/pair_coul_long.h | 25 +-
src/KSPACE/pair_coul_msm.cpp | 212 +
src/KSPACE/pair_coul_msm.h | 67 +
src/KSPACE/pair_lj_charmm_coul_long.cpp | 810 +-
src/KSPACE/pair_lj_charmm_coul_long.h | 24 +-
src/KSPACE/pair_lj_charmm_coul_msm.cpp | 482 +
src/KSPACE/pair_lj_charmm_coul_msm.h | 77 +
src/KSPACE/pair_lj_cut_coul_long.cpp | 706 +-
src/KSPACE/pair_lj_cut_coul_long.h | 25 +-
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp | 522 -
src/KSPACE/pair_lj_cut_coul_long_tip4p.h | 97 -
src/KSPACE/pair_lj_cut_coul_msm.cpp | 424 +
src/KSPACE/pair_lj_cut_coul_msm.h | 68 +
src/KSPACE/pair_lj_cut_tip4p_long.cpp | 602 +
src/KSPACE/pair_lj_cut_tip4p_long.h | 105 +
src/KSPACE/pair_lj_long_coul_long.cpp | 1047 +
src/KSPACE/pair_lj_long_coul_long.h | 130 +
src/KSPACE/pair_lj_long_tip4p_long.cpp | 1617 +
src/KSPACE/pair_lj_long_tip4p_long.h | 121 +
src/KSPACE/pair_tip4p_long.cpp | 528 +
src/KSPACE/pair_tip4p_long.h | 100 +
src/KSPACE/pppm.cpp | 3740 +-
src/KSPACE/pppm.h | 160 +-
src/KSPACE/pppm_cg.cpp | 494 +-
src/KSPACE/pppm_cg.h | 6 +-
src/KSPACE/pppm_disp.cpp | 6700 ++
src/KSPACE/pppm_disp.h | 611 +
src/KSPACE/pppm_disp_tip4p.cpp | 519 +
src/KSPACE/pppm_disp_tip4p.h | 83 +
src/KSPACE/pppm_old.cpp | 2863 +
src/KSPACE/pppm_old.h | 246 +
src/KSPACE/pppm_stagger.cpp | 999 +
src/KSPACE/pppm_stagger.h | 110 +
src/KSPACE/pppm_tip4p.cpp | 314 +-
src/KSPACE/pppm_tip4p.h | 8 +-
src/KSPACE/remap.cpp | 206 +-
src/KSPACE/remap.h | 54 +-
src/KSPACE/remap_wrap.cpp | 18 +-
src/KSPACE/remap_wrap.h | 4 +-
src/MAKE/Makefile.altix | 29 +-
src/MAKE/Makefile.bgl | 29 +-
src/MAKE/Makefile.chama | 104 +
src/MAKE/Makefile.cygwin | 33 +-
src/MAKE/Makefile.encanto | 29 +-
src/MAKE/Makefile.fedora | 39 +-
src/MAKE/Makefile.fedora_debug | 109 +
src/MAKE/Makefile.fedora_fpic | 39 +-
src/MAKE/Makefile.fedora_gp | 37 +-
src/MAKE/Makefile.fink | 33 +-
src/MAKE/Makefile.g++ | 31 +-
src/MAKE/Makefile.g++3 | 29 +-
src/MAKE/Makefile.glory | 29 +-
src/MAKE/Makefile.jaguar | 31 +-
src/MAKE/Makefile.lam | 29 +-
src/MAKE/Makefile.linux | 29 +-
src/MAKE/Makefile.mac | 33 +-
src/MAKE/Makefile.mac_mpi | 35 +-
src/MAKE/Makefile.mingw | 10 +-
src/MAKE/Makefile.mkl | 29 +-
src/MAKE/Makefile.odin | 29 +-
src/MAKE/Makefile.openmpi | 31 +-
src/MAKE/Makefile.pgi | 32 +-
src/MAKE/Makefile.power5 | 29 +-
src/MAKE/Makefile.qed | 29 +-
src/MAKE/Makefile.redsky | 57 +-
src/MAKE/Makefile.sdsc | 29 +-
src/MAKE/Makefile.seaborg | 29 +-
src/MAKE/Makefile.serial | 38 +-
src/MAKE/Makefile.serial_debug | 33 +-
src/MAKE/Makefile.serial_icc | 94 -
src/MAKE/Makefile.sgi | 29 +-
src/MAKE/Makefile.solaris | 33 +-
src/MAKE/Makefile.spirit | 29 +-
src/MAKE/Makefile.storm | 27 +-
src/MAKE/Makefile.tacc | 29 +-
src/MAKE/Makefile.tbird | 29 +-
src/MAKE/Makefile.tesla | 33 +-
src/MAKE/Makefile.tunnison | 29 +-
src/MAKE/Makefile.ubuntuVTK | 10 +-
src/MAKE/Makefile.xe6 | 29 +-
src/MAKE/Makefile.xt3 | 31 +-
src/MAKE/Makefile.xt5 | 29 +-
src/MANYBODY/Install.sh | 59 -
src/MANYBODY/fix_qeq_comb.cpp | 157 +-
src/MANYBODY/fix_qeq_comb.h | 7 +-
src/MANYBODY/pair_adp.cpp | 219 +-
src/MANYBODY/pair_adp.h | 6 +-
src/MANYBODY/pair_airebo.cpp | 3921 +-
src/MANYBODY/pair_airebo.h | 16 +-
src/MANYBODY/pair_bop.cpp | 9543 ++
src/MANYBODY/pair_bop.h | 265 +
src/MANYBODY/pair_comb.cpp | 855 +-
src/MANYBODY/pair_comb.h | 65 +-
src/MANYBODY/pair_comb3.cpp | 4058 +
src/MANYBODY/pair_comb3.h | 333 +
src/MANYBODY/pair_eam.cpp | 236 +-
src/MANYBODY/pair_eam.h | 4 +-
src/MANYBODY/pair_eam_alloy.cpp | 28 +-
src/MANYBODY/pair_eam_alloy.h | 2 +-
src/MANYBODY/pair_eam_fs.cpp | 32 +-
src/MANYBODY/pair_eam_fs.h | 2 +-
src/MANYBODY/pair_eim.cpp | 111 +-
src/MANYBODY/pair_eim.h | 6 +-
src/MANYBODY/pair_lcbop.cpp | 1292 +
src/MANYBODY/pair_lcbop.h | 207 +
src/MANYBODY/pair_nb3b_harmonic.cpp | 532 +
src/MANYBODY/pair_nb3b_harmonic.h | 64 +
src/MANYBODY/pair_rebo.cpp | 2 +-
src/MANYBODY/pair_rebo.h | 2 +-
src/MANYBODY/pair_sw.cpp | 158 +-
src/MANYBODY/pair_sw.h | 12 +-
src/MANYBODY/pair_tersoff.cpp | 201 +-
src/MANYBODY/pair_tersoff.h | 50 +-
src/MANYBODY/pair_tersoff_mod.cpp | 361 +
src/MANYBODY/pair_tersoff_mod.h | 79 +
src/MANYBODY/pair_tersoff_zbl.cpp | 74 +-
src/MANYBODY/pair_tersoff_zbl.h | 10 +-
src/MC/Install.sh | 31 -
src/MC/fix_bond_break.cpp | 50 +-
src/MC/fix_bond_break.h | 2 +-
src/MC/fix_bond_create.cpp | 123 +-
src/MC/fix_bond_create.h | 6 +-
src/MC/fix_bond_swap.cpp | 309 +-
src/MC/fix_bond_swap.h | 4 +-
src/MC/fix_gcmc.cpp | 1275 +-
src/MC/fix_gcmc.h | 158 +-
src/MC/pair_dsmc.cpp | 95 +-
src/MC/pair_dsmc.h | 6 +-
src/MEAM/Install.sh | 39 +-
src/MEAM/pair_meam.cpp | 85 +-
src/MEAM/pair_meam.h | 42 +-
src/MISC/compute_msd_nongauss.cpp | 106 +
src/MISC/compute_msd_nongauss.h | 51 +
src/MISC/compute_ti.cpp | 241 +
src/MISC/compute_ti.h | 83 +
src/MISC/fix_efield.cpp | 445 +
src/MISC/fix_efield.h | 106 +
src/MISC/fix_evaporate.cpp | 386 +
src/{ => MISC}/fix_evaporate.h | 0
src/MISC/fix_gld.cpp | 641 +
src/MISC/fix_gld.h | 81 +
src/MISC/fix_orient_fcc.cpp | 607 +
src/{ => MISC}/fix_orient_fcc.h | 0
src/MISC/fix_thermal_conductivity.cpp | 330 +
src/{ => MISC}/fix_thermal_conductivity.h | 0
src/MISC/fix_ttm.cpp | 685 +
src/{ => MISC}/fix_ttm.h | 0
src/MISC/fix_viscosity.cpp | 309 +
src/{ => MISC}/fix_viscosity.h | 0
src/MISC/pair_nm_cut.cpp | 433 +
src/MISC/pair_nm_cut.h | 57 +
src/MISC/pair_nm_cut_coul_cut.cpp | 506 +
src/MISC/pair_nm_cut_coul_cut.h | 78 +
src/MISC/pair_nm_cut_coul_long.cpp | 590 +
src/MISC/pair_nm_cut_coul_long.h | 84 +
src/MOLECULE/Install.sh | 143 -
src/MOLECULE/angle_charmm.cpp | 34 +-
src/MOLECULE/angle_charmm.h | 3 +-
src/MOLECULE/angle_cosine.cpp | 26 +-
src/MOLECULE/angle_cosine.h | 3 +-
src/MOLECULE/angle_cosine_delta.cpp | 28 +-
src/MOLECULE/angle_cosine_delta.h | 2 +-
src/MOLECULE/angle_cosine_periodic.cpp | 41 +-
src/MOLECULE/angle_cosine_periodic.h | 5 +-
src/MOLECULE/angle_cosine_squared.cpp | 32 +-
src/MOLECULE/angle_cosine_squared.h | 3 +-
src/MOLECULE/angle_harmonic.cpp | 28 +-
src/MOLECULE/angle_harmonic.h | 3 +-
src/MOLECULE/angle_hybrid.cpp | 367 -
src/MOLECULE/angle_hybrid.h | 95 -
src/MOLECULE/angle_table.cpp | 86 +-
src/MOLECULE/angle_table.h | 4 +-
src/MOLECULE/atom_vec_angle.cpp | 389 +-
src/MOLECULE/atom_vec_angle.h | 13 +-
src/MOLECULE/atom_vec_bond.cpp | 353 +-
src/MOLECULE/atom_vec_bond.h | 13 +-
src/MOLECULE/atom_vec_full.cpp | 581 +-
src/MOLECULE/atom_vec_full.h | 13 +-
src/MOLECULE/atom_vec_molecular.cpp | 571 +-
src/MOLECULE/atom_vec_molecular.h | 13 +-
src/MOLECULE/bond_fene.cpp | 32 +-
src/MOLECULE/bond_fene.h | 5 +-
src/MOLECULE/bond_fene_expand.cpp | 34 +-
src/MOLECULE/bond_fene_expand.h | 5 +-
src/MOLECULE/bond_harmonic.cpp | 28 +-
src/MOLECULE/bond_harmonic.h | 5 +-
src/MOLECULE/bond_morse.cpp | 26 +-
src/MOLECULE/bond_morse.h | 5 +-
src/MOLECULE/bond_nonlinear.cpp | 24 +-
src/MOLECULE/bond_nonlinear.h | 5 +-
src/MOLECULE/bond_quartic.cpp | 62 +-
src/MOLECULE/bond_quartic.h | 5 +-
src/MOLECULE/bond_table.cpp | 66 +-
src/MOLECULE/bond_table.h | 6 +-
src/MOLECULE/dihedral_charmm.cpp | 126 +-
src/MOLECULE/dihedral_charmm.h | 5 +-
src/MOLECULE/dihedral_harmonic.cpp | 96 +-
src/MOLECULE/dihedral_harmonic.h | 3 +-
src/MOLECULE/dihedral_helix.cpp | 58 +-
src/MOLECULE/dihedral_helix.h | 2 +-
src/MOLECULE/dihedral_hybrid.cpp | 298 -
src/MOLECULE/dihedral_hybrid.h | 79 -
src/MOLECULE/dihedral_multi_harmonic.cpp | 58 +-
src/MOLECULE/dihedral_multi_harmonic.h | 2 +-
src/MOLECULE/dihedral_opls.cpp | 70 +-
src/MOLECULE/dihedral_opls.h | 5 +-
src/MOLECULE/improper_cvff.cpp | 75 +-
src/MOLECULE/improper_cvff.h | 5 +-
src/MOLECULE/improper_harmonic.cpp | 66 +-
src/MOLECULE/improper_harmonic.h | 3 +-
src/MOLECULE/improper_hybrid.cpp | 286 -
src/MOLECULE/improper_hybrid.h | 78 -
src/MOLECULE/improper_umbrella.cpp | 55 +-
src/MOLECULE/improper_umbrella.h | 2 +-
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 339 +-
src/MOLECULE/pair_hbond_dreiding_lj.h | 2 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 310 +-
src/MOLECULE/pair_hbond_dreiding_morse.h | 2 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 236 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.h | 6 +-
.../pair_lj_charmm_coul_charmm_implicit.cpp | 158 +-
src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h | 2 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 734 +
src/MOLECULE/pair_lj_cut_tip4p_cut.h | 112 +
src/MOLECULE/pair_tip4p_cut.cpp | 551 +
src/MOLECULE/pair_tip4p_cut.h | 103 +
src/Make.py | 15 +-
src/Make.sh | 116 +-
src/Makefile | 65 +-
src/Makefile.lib | 4 +-
src/Makefile.list | 3 -
src/Makefile.shlib | 43 +
src/OPT/Install.sh | 90 +-
src/OPT/Package.sh | 50 -
src/OPT/pair_eam_alloy_opt.cpp | 4 +-
src/OPT/pair_eam_alloy_opt.h | 2 +-
src/OPT/pair_eam_fs_opt.cpp | 4 +-
src/OPT/pair_eam_fs_opt.h | 2 +-
src/OPT/pair_eam_opt.cpp | 257 +-
src/OPT/pair_eam_opt.h | 2 +-
src/OPT/pair_lj_charmm_coul_long_opt.cpp | 397 +-
src/OPT/pair_lj_charmm_coul_long_opt.h | 4 +-
src/OPT/pair_lj_cut_coul_long_opt.cpp | 132 +-
src/OPT/pair_lj_cut_coul_long_opt.h | 4 +-
src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp | 459 -
src/OPT/pair_lj_cut_coul_long_tip4p_opt.h | 59 -
src/OPT/pair_lj_cut_opt.cpp | 162 +-
src/OPT/pair_lj_cut_opt.h | 2 +-
src/OPT/pair_lj_cut_tip4p_long_opt.cpp | 470 +
src/OPT/pair_lj_cut_tip4p_long_opt.h | 59 +
src/OPT/pair_lj_long_coul_long_opt.cpp | 880 +
src/OPT/pair_lj_long_coul_long_opt.h | 48 +
src/OPT/pair_morse_opt.cpp | 154 +-
src/OPT/pair_morse_opt.h | 2 +-
src/PERI/Install.sh | 31 -
src/PERI/atom_vec_peri.cpp | 349 +-
src/PERI/atom_vec_peri.h | 13 +-
src/PERI/compute_damage_atom.cpp | 6 +-
src/PERI/compute_damage_atom.h | 2 +-
src/PERI/fix_peri_neigh.cpp | 126 +-
src/PERI/fix_peri_neigh.h | 12 +-
src/PERI/pair_peri_lps.cpp | 302 +-
src/PERI/pair_peri_lps.h | 45 +-
src/PERI/pair_peri_pmb.cpp | 86 +-
src/PERI/pair_peri_pmb.h | 4 +-
src/PERI/pair_peri_ves.cpp | 724 +
src/PERI/pair_peri_ves.h | 109 +
src/POEMS/Install.sh | 41 +-
src/POEMS/fix_poems.cpp | 390 +-
src/POEMS/fix_poems.h | 8 +-
src/Package.sh | 58 +-
src/Purge.list | 256 +
src/REAX/Install.sh | 47 +-
src/REAX/fix_reax_bonds.cpp | 131 +-
src/REAX/fix_reax_bonds.h | 2 +-
src/REAX/pair_reax.cpp | 264 +-
src/REAX/pair_reax.h | 14 +-
src/REAX/pair_reax_fortran.h | 37 +-
src/REPLICA/Install.sh | 51 -
src/REPLICA/compute_event_displace.cpp | 39 +-
src/REPLICA/compute_event_displace.h | 2 +-
src/REPLICA/fix_event.cpp | 26 +-
src/REPLICA/fix_event.h | 4 +-
src/REPLICA/fix_event_prd.cpp | 8 +-
src/REPLICA/fix_event_prd.h | 2 +-
src/REPLICA/fix_event_tad.cpp | 8 +-
src/REPLICA/fix_event_tad.h | 4 +-
src/REPLICA/fix_neb.cpp | 82 +-
src/REPLICA/fix_neb.h | 2 +-
src/REPLICA/neb.cpp | 319 +-
src/REPLICA/neb.h | 6 +-
src/REPLICA/prd.cpp | 193 +-
src/REPLICA/prd.h | 14 +-
src/REPLICA/tad.cpp | 369 +-
src/REPLICA/tad.h | 13 +-
src/REPLICA/temper.cpp | 70 +-
src/REPLICA/temper.h | 2 +-
src/REPLICA/verlet_split.cpp | 181 +-
src/REPLICA/verlet_split.h | 4 +-
src/RIGID/compute_erotate_rigid.cpp | 75 +
src/RIGID/compute_erotate_rigid.h | 56 +
src/RIGID/compute_ke_rigid.cpp | 73 +
src/RIGID/compute_ke_rigid.h | 52 +
src/RIGID/fix_rigid.cpp | 2564 +
src/RIGID/fix_rigid.h | 257 +
src/RIGID/fix_rigid_nh.cpp | 1430 +
src/RIGID/fix_rigid_nh.h | 183 +
src/RIGID/fix_rigid_nph.cpp | 90 +
src/RIGID/fix_rigid_nph.h | 49 +
src/RIGID/fix_rigid_npt.cpp | 100 +
src/RIGID/fix_rigid_npt.h | 63 +
src/RIGID/fix_rigid_nve.cpp | 28 +
src/RIGID/fix_rigid_nve.h | 36 +
src/RIGID/fix_rigid_nvt.cpp | 50 +
src/RIGID/fix_rigid_nvt.h | 62 +
src/RIGID/fix_rigid_small.cpp | 3140 +
src/RIGID/fix_rigid_small.h | 248 +
src/SHOCK/Install.sh | 27 -
src/SHOCK/fix_append_atoms.cpp | 204 +-
src/SHOCK/fix_append_atoms.h | 27 +-
src/SHOCK/fix_msst.cpp | 235 +-
src/SHOCK/fix_msst.h | 14 +-
src/SHOCK/fix_nphug.cpp | 78 +-
src/SHOCK/fix_nphug.h | 4 +-
src/SHOCK/fix_wall_piston.cpp | 120 +-
src/SHOCK/fix_wall_piston.h | 10 +-
src/SRD/Install.sh | 19 -
src/SRD/fix_srd.cpp | 1244 +-
src/SRD/fix_srd.h | 31 +-
src/SRD/fix_wall_srd.cpp | 44 +-
src/SRD/fix_wall_srd.h | 14 +-
src/STUBS/Makefile | 22 +-
src/STUBS/Makefile.mingw32-cross | 37 +
src/STUBS/Makefile.mingw64-cross | 37 +
src/STUBS/mpi.c | 9 +
src/STUBS/mpi.h | 27 +-
src/USER-ATC/Install.sh | 44 +-
src/USER-ATC/fix_atc.cpp | 658 +-
src/USER-ATC/fix_atc.h | 111 +-
src/USER-AWPMD/Install.sh | 49 +-
src/USER-AWPMD/atom_vec_wavepacket.cpp | 554 +-
src/USER-AWPMD/atom_vec_wavepacket.h | 29 +-
src/USER-AWPMD/fix_nve_awpmd.cpp | 17 +-
src/USER-AWPMD/fix_nve_awpmd.h | 2 +-
src/USER-AWPMD/pair_awpmd_cut.cpp | 138 +-
src/USER-AWPMD/pair_awpmd_cut.h | 18 +-
src/USER-CG-CMM/Install.sh | 94 +-
src/USER-CG-CMM/Package.sh | 38 -
src/USER-CG-CMM/angle_cg_cmm.cpp | 436 -
src/USER-CG-CMM/angle_cg_cmm.h | 55 -
src/USER-CG-CMM/angle_sdk.cpp | 120 +-
src/USER-CG-CMM/angle_sdk.h | 9 +-
src/USER-CG-CMM/cg_cmm_parms.cpp | 43 -
src/USER-CG-CMM/cg_cmm_parms.h | 43 -
src/USER-CG-CMM/lj_sdk_common.h | 7 +-
src/USER-CG-CMM/pair_cg_cmm.cpp | 174 -
src/USER-CG-CMM/pair_cg_cmm.h | 51 -
src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp | 241 -
src/USER-CG-CMM/pair_cg_cmm_coul_cut.h | 53 -
src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp | 452 -
src/USER-CG-CMM/pair_cg_cmm_coul_long.h | 56 -
src/USER-CG-CMM/pair_cmm_common.cpp | 71 +-
src/USER-CG-CMM/pair_cmm_common.h | 108 +-
src/USER-CG-CMM/pair_lj_sdk.cpp | 182 +-
src/USER-CG-CMM/pair_lj_sdk.h | 8 +-
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp | 411 +-
src/USER-CG-CMM/pair_lj_sdk_coul_long.h | 15 +-
src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp | 307 +
src/USER-CG-CMM/pair_lj_sdk_coul_msm.h | 48 +
src/USER-COLVARS/Install.sh | 64 +
src/USER-COLVARS/README | 47 +
src/USER-COLVARS/colvarproxy_lammps.cpp | 461 +
src/USER-COLVARS/colvarproxy_lammps.h | 147 +
src/USER-COLVARS/fix_colvars.cpp | 946 +
src/USER-COLVARS/fix_colvars.h | 146 +
src/USER-COLVARS/group_ndx.cpp | 174 +
src/USER-COLVARS/group_ndx.h | 55 +
src/USER-CUDA/Install.sh | 488 +-
src/USER-CUDA/atom_vec_angle_cuda.cpp | 240 +-
src/USER-CUDA/atom_vec_angle_cuda.h | 16 +-
src/USER-CUDA/atom_vec_atomic_cuda.cpp | 164 +-
src/USER-CUDA/atom_vec_atomic_cuda.h | 18 +-
src/USER-CUDA/atom_vec_charge_cuda.cpp | 166 +-
src/USER-CUDA/atom_vec_charge_cuda.h | 16 +-
src/USER-CUDA/atom_vec_full_cuda.cpp | 273 +-
src/USER-CUDA/atom_vec_full_cuda.h | 16 +-
src/USER-CUDA/comm_cuda.cpp | 819 +-
src/USER-CUDA/comm_cuda.h | 8 +-
src/USER-CUDA/compute_pe_cuda.cpp | 18 +-
src/USER-CUDA/compute_pe_cuda.h | 16 +-
src/USER-CUDA/compute_pressure_cuda.cpp | 20 +-
src/USER-CUDA/compute_pressure_cuda.h | 16 +-
src/USER-CUDA/compute_temp_cuda.cpp | 60 +-
src/USER-CUDA/compute_temp_cuda.h | 25 +-
src/USER-CUDA/compute_temp_partial_cuda.cpp | 88 +-
src/USER-CUDA/compute_temp_partial_cuda.h | 23 +-
src/USER-CUDA/cuda.cpp | 1603 +-
src/USER-CUDA/cuda.h | 238 +-
src/USER-CUDA/cuda_data.h | 1286 +-
src/USER-CUDA/cuda_modify_flags.h | 14 +-
src/USER-CUDA/cuda_neigh_list.cpp | 251 +-
src/USER-CUDA/cuda_neigh_list.h | 94 +-
src/USER-CUDA/domain_cuda.cpp | 215 +-
src/USER-CUDA/domain_cuda.h | 4 +-
src/USER-CUDA/fft3d_cuda.cpp | 128 +-
src/USER-CUDA/fft3d_cuda.h | 62 +-
src/USER-CUDA/fft3d_wrap_cuda.cpp | 44 +-
src/USER-CUDA/fft3d_wrap_cuda.h | 18 +-
src/USER-CUDA/fix_addforce_cuda.cpp | 24 +-
src/USER-CUDA/fix_addforce_cuda.h | 16 +-
src/USER-CUDA/fix_aveforce_cuda.cpp | 168 +-
src/USER-CUDA/fix_aveforce_cuda.h | 23 +-
src/USER-CUDA/fix_enforce2d_cuda.cpp | 38 +-
src/USER-CUDA/fix_enforce2d_cuda.h | 14 +-
src/USER-CUDA/fix_freeze_cuda.cpp | 20 +-
src/USER-CUDA/fix_freeze_cuda.h | 16 +-
src/USER-CUDA/fix_gravity_cuda.cpp | 34 +-
src/USER-CUDA/fix_gravity_cuda.h | 14 +-
src/USER-CUDA/fix_nh_cuda.cpp | 656 +-
src/USER-CUDA/fix_nh_cuda.h | 8 +-
src/USER-CUDA/fix_npt_cuda.cpp | 6 +-
src/USER-CUDA/fix_npt_cuda.h | 2 +-
src/USER-CUDA/fix_nve_cuda.cpp | 110 +-
src/USER-CUDA/fix_nve_cuda.h | 50 +-
src/USER-CUDA/fix_nvt_cuda.cpp | 4 +-
src/USER-CUDA/fix_nvt_cuda.h | 2 +-
src/USER-CUDA/fix_set_force_cuda.cpp | 44 +-
src/USER-CUDA/fix_set_force_cuda.h | 18 +-
src/USER-CUDA/fix_shake_cuda.cpp | 2651 +-
src/USER-CUDA/fix_shake_cuda.h | 24 +-
src/USER-CUDA/fix_temp_berendsen_cuda.cpp | 57 +-
src/USER-CUDA/fix_temp_berendsen_cuda.h | 14 +-
src/USER-CUDA/fix_temp_rescale_cuda.cpp | 50 +-
src/USER-CUDA/fix_temp_rescale_cuda.h | 14 +-
src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp | 64 +-
src/USER-CUDA/fix_temp_rescale_limit_cuda.h | 14 +-
src/USER-CUDA/fix_viscous_cuda.cpp | 18 +-
src/USER-CUDA/fix_viscous_cuda.h | 14 +-
src/USER-CUDA/modify_cuda.cpp | 240 +-
src/USER-CUDA/modify_cuda.h | 2 +-
src/USER-CUDA/neigh_full_cuda.cpp | 257 +-
src/USER-CUDA/neighbor_cuda.cpp | 199 +-
src/USER-CUDA/neighbor_cuda.h | 4 +-
src/USER-CUDA/pair_born_coul_long_cuda.cpp | 126 +-
src/USER-CUDA/pair_born_coul_long_cuda.h | 40 +-
src/USER-CUDA/pair_buck_coul_cut_cuda.cpp | 126 +-
src/USER-CUDA/pair_buck_coul_cut_cuda.h | 40 +-
src/USER-CUDA/pair_buck_coul_long_cuda.cpp | 118 +-
src/USER-CUDA/pair_buck_coul_long_cuda.h | 40 +-
src/USER-CUDA/pair_buck_cuda.cpp | 116 +-
src/USER-CUDA/pair_buck_cuda.h | 40 +-
src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.cpp | 201 -
src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.h | 58 -
src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.cpp | 201 -
src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.h | 58 -
src/USER-CUDA/pair_cg_cmm_coul_long_cuda.cpp | 203 -
src/USER-CUDA/pair_cg_cmm_coul_long_cuda.h | 58 -
src/USER-CUDA/pair_cg_cmm_cuda.cpp | 198 -
src/USER-CUDA/pair_cg_cmm_cuda.h | 64 -
src/USER-CUDA/pair_eam_alloy_cuda.cpp | 24 +-
src/USER-CUDA/pair_eam_alloy_cuda.h | 2 +-
src/USER-CUDA/pair_eam_cuda.cpp | 250 +-
src/USER-CUDA/pair_eam_cuda.h | 58 +-
src/USER-CUDA/pair_eam_fs_cuda.cpp | 28 +-
src/USER-CUDA/pair_eam_fs_cuda.h | 2 +-
src/USER-CUDA/pair_gran_hooke_cuda.cpp | 136 +-
src/USER-CUDA/pair_gran_hooke_cuda.h | 40 +-
src/USER-CUDA/pair_lj96_cut_cuda.cpp | 114 +-
src/USER-CUDA/pair_lj96_cut_cuda.h | 40 +-
src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp | 154 +-
src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h | 48 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda.cpp | 142 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda.h | 48 +-
src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp | 148 +-
src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h | 48 +-
src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp | 114 +-
src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h | 40 +-
src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp | 102 +-
src/USER-CUDA/pair_lj_class2_coul_long_cuda.h | 40 +-
src/USER-CUDA/pair_lj_class2_cuda.cpp | 102 +-
src/USER-CUDA/pair_lj_class2_cuda.h | 40 +-
src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp | 114 +-
src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h | 40 +-
src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp | 116 +-
src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h | 40 +-
src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp | 112 +-
src/USER-CUDA/pair_lj_cut_coul_long_cuda.h | 40 +-
src/USER-CUDA/pair_lj_cut_cuda.cpp | 112 +-
src/USER-CUDA/pair_lj_cut_cuda.h | 40 +-
src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp | 112 +-
src/USER-CUDA/pair_lj_cut_experimental_cuda.h | 40 +-
src/USER-CUDA/pair_lj_expand_cuda.cpp | 120 +-
src/USER-CUDA/pair_lj_expand_cuda.h | 40 +-
.../pair_lj_gromacs_coul_gromacs_cuda.cpp | 172 +-
src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h | 58 +-
src/USER-CUDA/pair_lj_gromacs_cuda.cpp | 164 +-
src/USER-CUDA/pair_lj_gromacs_cuda.h | 58 +-
src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.cpp | 201 -
src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.h | 58 -
src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.cpp | 201 -
src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.h | 58 -
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp | 130 +-
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h | 42 +-
src/USER-CUDA/pair_lj_sdk_cuda.cpp | 128 +-
src/USER-CUDA/pair_lj_sdk_cuda.h | 52 +-
src/USER-CUDA/pair_lj_smooth_cuda.cpp | 164 +-
src/USER-CUDA/pair_lj_smooth_cuda.h | 58 +-
src/USER-CUDA/pair_morse_cuda.cpp | 112 +-
src/USER-CUDA/pair_morse_cuda.h | 40 +-
src/USER-CUDA/pair_sw_cuda.cpp | 88 +-
src/USER-CUDA/pair_sw_cuda.h | 48 +-
src/USER-CUDA/pair_tersoff_cuda.cpp | 88 +-
src/USER-CUDA/pair_tersoff_cuda.h | 48 +-
src/USER-CUDA/pair_tersoff_zbl_cuda.cpp | 34 +-
src/USER-CUDA/pair_tersoff_zbl_cuda.h | 32 +-
src/USER-CUDA/pppm_cuda.cpp | 489 +-
src/USER-CUDA/pppm_cuda.h | 55 +-
src/USER-CUDA/verlet_cuda.cpp | 1852 +-
src/USER-CUDA/verlet_cuda.h | 50 +-
src/USER-EFF/Install.sh | 73 -
src/USER-EFF/atom_vec_electron.cpp | 484 +-
src/USER-EFF/atom_vec_electron.h | 29 +-
src/USER-EFF/compute_ke_atom_eff.cpp | 12 +-
src/USER-EFF/compute_ke_atom_eff.h | 4 +-
src/USER-EFF/compute_ke_eff.cpp | 6 +-
src/USER-EFF/compute_ke_eff.h | 10 +-
src/USER-EFF/compute_temp_deform_eff.cpp | 51 +-
src/USER-EFF/compute_temp_deform_eff.h | 2 +-
src/USER-EFF/compute_temp_eff.cpp | 20 +-
src/USER-EFF/compute_temp_eff.h | 15 +-
src/USER-EFF/compute_temp_region_eff.cpp | 36 +-
src/USER-EFF/compute_temp_region_eff.h | 5 +-
src/USER-EFF/fix_langevin_eff.cpp | 185 +-
src/USER-EFF/fix_langevin_eff.h | 3 +-
src/USER-EFF/fix_nh_eff.cpp | 12 +-
src/USER-EFF/fix_nh_eff.h | 2 +-
src/USER-EFF/fix_nph_eff.cpp | 6 +-
src/USER-EFF/fix_nph_eff.h | 2 +-
src/USER-EFF/fix_npt_eff.cpp | 6 +-
src/USER-EFF/fix_npt_eff.h | 2 +-
src/USER-EFF/fix_nve_eff.cpp | 13 +-
src/USER-EFF/fix_nve_eff.h | 2 +-
src/USER-EFF/fix_nvt_eff.cpp | 4 +-
src/USER-EFF/fix_nvt_eff.h | 2 +-
src/USER-EFF/fix_nvt_sllod_eff.cpp | 8 +-
src/USER-EFF/fix_nvt_sllod_eff.h | 2 +-
src/USER-EFF/fix_temp_rescale_eff.cpp | 41 +-
src/USER-EFF/fix_temp_rescale_eff.h | 2 +-
src/USER-EFF/pair_eff_cut.cpp | 485 +-
src/USER-EFF/pair_eff_cut.h | 17 +-
src/USER-EFF/pair_eff_inline.h | 162 +-
src/USER-EWALDN/Install.sh | 33 -
src/USER-EWALDN/README | 29 -
src/USER-EWALDN/ewald_n.cpp | 1222 -
src/USER-EWALDN/ewald_n.h | 95 -
src/USER-EWALDN/math_complex.h | 73 -
src/USER-EWALDN/math_vector.h | 448 -
src/USER-EWALDN/pair_buck_coul.cpp | 1168 -
src/USER-EWALDN/pair_buck_coul.h | 76 -
src/USER-EWALDN/pair_lj_coul.cpp | 1160 -
src/USER-EWALDN/pair_lj_coul.h | 75 -
src/USER-LB/README | 54 +
src/USER-LB/fix_lb_fluid.cpp | 3362 +
src/USER-LB/fix_lb_fluid.h | 167 +
src/USER-LB/fix_lb_momentum.cpp | 296 +
src/USER-LB/fix_lb_momentum.h | 45 +
src/USER-LB/fix_lb_pc.cpp | 472 +
src/USER-LB/fix_lb_pc.h | 61 +
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 1688 +
src/USER-LB/fix_lb_rigid_pc_sphere.h | 110 +
src/USER-LB/fix_lb_viscous.cpp | 146 +
src/USER-LB/fix_lb_viscous.h | 49 +
src/USER-MISC/Install.sh | 115 +-
src/USER-MISC/README | 14 +
src/USER-MISC/angle_cosine_shift.cpp | 46 +-
src/USER-MISC/angle_cosine_shift.h | 3 +-
src/USER-MISC/angle_cosine_shift_exp.cpp | 54 +-
src/USER-MISC/angle_cosine_shift_exp.h | 3 +-
src/USER-MISC/angle_dipole.cpp | 37 +-
src/USER-MISC/angle_dipole.h | 3 +-
src/USER-MISC/angle_fourier.cpp | 278 +
src/USER-MISC/angle_fourier.h | 49 +
src/USER-MISC/angle_fourier_simple.cpp | 283 +
src/USER-MISC/angle_fourier_simple.h | 49 +
src/USER-MISC/angle_quartic.cpp | 289 +
src/USER-MISC/angle_quartic.h | 49 +
src/USER-MISC/bond_harmonic_shift.cpp | 32 +-
src/USER-MISC/bond_harmonic_shift.h | 6 +-
src/USER-MISC/bond_harmonic_shift_cut.cpp | 38 +-
src/USER-MISC/bond_harmonic_shift_cut.h | 6 +-
src/USER-MISC/compute_ackland_atom.cpp | 194 +-
src/USER-MISC/compute_ackland_atom.h | 2 +-
src/USER-MISC/compute_basal_atom.cpp | 542 +
src/USER-MISC/compute_basal_atom.h | 50 +
src/USER-MISC/compute_temp_rotate.cpp | 75 +-
src/USER-MISC/compute_temp_rotate.h | 3 +-
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 66 +-
src/USER-MISC/dihedral_cosine_shift_exp.h | 2 +-
src/USER-MISC/dihedral_fourier.cpp | 407 +
src/USER-MISC/dihedral_fourier.h | 49 +
src/USER-MISC/dihedral_nharmonic.cpp | 335 +
src/USER-MISC/dihedral_nharmonic.h | 47 +
src/USER-MISC/dihedral_quadratic.cpp | 334 +
src/USER-MISC/dihedral_quadratic.h | 47 +
src/USER-MISC/dihedral_table.cpp | 1192 +-
src/USER-MISC/dihedral_table.h | 235 +-
src/USER-MISC/fix_addtorque.cpp | 61 +-
src/USER-MISC/fix_addtorque.h | 2 +-
src/USER-MISC/fix_imd.cpp | 221 +-
src/USER-MISC/fix_imd.h | 46 +-
src/USER-MISC/fix_smd.cpp | 150 +-
src/USER-MISC/fix_smd.h | 4 +-
src/USER-MISC/fix_ti_rs.cpp | 197 +
src/USER-MISC/fix_ti_rs.h | 66 +
src/USER-MISC/fix_ti_spring.cpp | 365 +
src/USER-MISC/fix_ti_spring.h | 94 +
src/USER-MISC/improper_cossq.cpp | 313 +
src/USER-MISC/improper_cossq.h | 45 +
src/USER-MISC/improper_fourier.cpp | 345 +
src/USER-MISC/improper_fourier.h | 51 +
src/USER-MISC/improper_ring.cpp | 340 +
src/USER-MISC/improper_ring.h | 46 +
src/USER-MISC/pair_cdeam.cpp | 1098 +-
src/USER-MISC/pair_cdeam.h | 70 +-
src/USER-MISC/pair_coul_diel.cpp | 104 +-
src/USER-MISC/pair_coul_diel.h | 2 +-
src/USER-MISC/pair_dipole_sf.cpp | 504 -
src/USER-MISC/pair_dipole_sf.h | 54 -
src/USER-MISC/pair_edip.cpp | 246 +-
src/USER-MISC/pair_edip.h | 11 +-
src/USER-MISC/pair_gauss_cut.cpp | 113 +-
src/USER-MISC/pair_gauss_cut.h | 2 +-
src/USER-MISC/pair_list.cpp | 425 +
src/USER-MISC/pair_list.h | 116 +
src/USER-MISC/pair_lj_sf.cpp | 141 +-
src/USER-MISC/pair_lj_sf.h | 2 +-
src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 510 +
src/USER-MISC/pair_lj_sf_dipole_sf.h | 54 +
src/USER-MISC/pair_meam_spline.cpp | 694 +-
src/USER-MISC/pair_meam_spline.h | 444 +-
src/USER-MISC/pair_meam_sw_spline.cpp | 999 +
src/USER-MISC/pair_meam_sw_spline.h | 510 +
src/USER-MISC/pair_tersoff_table.cpp | 621 +-
src/USER-MISC/pair_tersoff_table.h | 20 +-
src/USER-MOLFILE/Install.sh | 60 +
src/USER-MOLFILE/Makefile.lammps | 37 +
src/USER-MOLFILE/README | 40 +
src/USER-MOLFILE/dump_molfile.cpp | 461 +
src/USER-MOLFILE/dump_molfile.h | 107 +
src/USER-MOLFILE/molfile_interface.cpp | 1223 +
src/USER-MOLFILE/molfile_interface.h | 161 +
src/USER-MOLFILE/molfile_plugin.h | 890 +
src/USER-MOLFILE/reader_molfile.cpp | 364 +
src/USER-MOLFILE/reader_molfile.h | 65 +
src/USER-MOLFILE/vmdplugin.h | 191 +
src/USER-OMP/Install.sh | 65 +-
src/USER-OMP/Package.sh | 46 -
src/USER-OMP/angle_charmm_omp.cpp | 82 +-
src/USER-OMP/angle_charmm_omp.h | 2 +-
src/USER-OMP/angle_class2_omp.cpp | 77 +-
src/USER-OMP/angle_class2_omp.h | 2 +-
src/USER-OMP/angle_cosine_delta_omp.cpp | 91 +-
src/USER-OMP/angle_cosine_delta_omp.h | 2 +-
src/USER-OMP/angle_cosine_omp.cpp | 71 +-
src/USER-OMP/angle_cosine_omp.h | 2 +-
src/USER-OMP/angle_cosine_periodic_omp.cpp | 81 +-
src/USER-OMP/angle_cosine_periodic_omp.h | 2 +-
src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 85 +-
src/USER-OMP/angle_cosine_shift_exp_omp.h | 2 +-
src/USER-OMP/angle_cosine_shift_omp.cpp | 84 +-
src/USER-OMP/angle_cosine_shift_omp.h | 2 +-
src/USER-OMP/angle_cosine_squared_omp.cpp | 77 +-
src/USER-OMP/angle_cosine_squared_omp.h | 2 +-
src/USER-OMP/angle_dipole_omp.cpp | 28 +-
src/USER-OMP/angle_dipole_omp.h | 2 +-
src/USER-OMP/angle_fourier_omp.cpp | 172 +
src/USER-OMP/angle_fourier_omp.h | 46 +
src/USER-OMP/angle_fourier_simple_omp.cpp | 189 +
src/USER-OMP/angle_fourier_simple_omp.h | 46 +
src/USER-OMP/angle_harmonic_omp.cpp | 75 +-
src/USER-OMP/angle_harmonic_omp.h | 2 +-
src/USER-OMP/angle_quartic_omp.cpp | 181 +
src/USER-OMP/angle_quartic_omp.h | 46 +
src/USER-OMP/angle_sdk_omp.cpp | 142 +-
src/USER-OMP/angle_sdk_omp.h | 2 +-
src/USER-OMP/angle_table_omp.cpp | 79 +-
src/USER-OMP/angle_table_omp.h | 2 +-
src/USER-OMP/bond_class2_omp.cpp | 56 +-
src/USER-OMP/bond_class2_omp.h | 2 +-
src/USER-OMP/bond_fene_expand_omp.cpp | 62 +-
src/USER-OMP/bond_fene_expand_omp.h | 2 +-
src/USER-OMP/bond_fene_omp.cpp | 62 +-
src/USER-OMP/bond_fene_omp.h | 2 +-
src/USER-OMP/bond_harmonic_omp.cpp | 56 +-
src/USER-OMP/bond_harmonic_omp.h | 2 +-
src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 59 +-
src/USER-OMP/bond_harmonic_shift_cut_omp.h | 2 +-
src/USER-OMP/bond_harmonic_shift_omp.cpp | 59 +-
src/USER-OMP/bond_harmonic_shift_omp.h | 2 +-
src/USER-OMP/bond_morse_omp.cpp | 56 +-
src/USER-OMP/bond_morse_omp.h | 2 +-
src/USER-OMP/bond_nonlinear_omp.cpp | 56 +-
src/USER-OMP/bond_nonlinear_omp.h | 2 +-
src/USER-OMP/bond_quartic_omp.cpp | 52 +-
src/USER-OMP/bond_quartic_omp.h | 2 +-
src/USER-OMP/bond_table_omp.cpp | 56 +-
src/USER-OMP/bond_table_omp.h | 2 +-
src/USER-OMP/dihedral_charmm_omp.cpp | 173 +-
src/USER-OMP/dihedral_charmm_omp.h | 2 +-
src/USER-OMP/dihedral_class2_omp.cpp | 218 +-
src/USER-OMP/dihedral_class2_omp.h | 2 +-
src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp | 130 +-
src/USER-OMP/dihedral_cosine_shift_exp_omp.h | 2 +-
src/USER-OMP/dihedral_fourier_omp.cpp | 275 +
src/USER-OMP/dihedral_fourier_omp.h | 46 +
src/USER-OMP/dihedral_harmonic_omp.cpp | 145 +-
src/USER-OMP/dihedral_harmonic_omp.h | 2 +-
src/USER-OMP/dihedral_helix_omp.cpp | 119 +-
src/USER-OMP/dihedral_helix_omp.h | 2 +-
src/USER-OMP/dihedral_multi_harmonic_omp.cpp | 129 +-
src/USER-OMP/dihedral_multi_harmonic_omp.h | 2 +-
src/USER-OMP/dihedral_nharmonic_omp.cpp | 275 +
src/USER-OMP/dihedral_nharmonic_omp.h | 46 +
src/USER-OMP/dihedral_opls_omp.cpp | 120 +-
src/USER-OMP/dihedral_opls_omp.h | 2 +-
src/USER-OMP/dihedral_quadratic_omp.cpp | 287 +
src/USER-OMP/dihedral_quadratic_omp.h | 46 +
src/USER-OMP/dihedral_table_omp.cpp | 176 +-
src/USER-OMP/dihedral_table_omp.h | 2 +-
src/USER-OMP/domain_omp.cpp | 187 +
src/USER-OMP/ewald_omp.cpp | 327 +-
src/USER-OMP/ewald_omp.h | 2 +-
src/USER-OMP/fix_gravity_omp.cpp | 63 +-
src/USER-OMP/fix_gravity_omp.h | 2 +-
src/USER-OMP/fix_nh_asphere_omp.cpp | 204 +
src/USER-OMP/fix_nh_asphere_omp.h | 51 +
src/USER-OMP/fix_nh_omp.cpp | 393 +
src/USER-OMP/fix_nh_omp.h | 153 +
src/USER-OMP/fix_nh_sphere_omp.cpp | 157 +
src/USER-OMP/fix_nh_sphere_omp.h | 46 +
src/USER-OMP/fix_nph_asphere_omp.cpp | 68 +
src/USER-OMP/fix_nph_asphere_omp.h | 48 +
src/USER-OMP/fix_nph_omp.cpp | 68 +
src/USER-OMP/fix_nph_omp.h | 48 +
src/USER-OMP/fix_nph_sphere_omp.cpp | 68 +
src/USER-OMP/fix_nph_sphere_omp.h | 48 +
src/USER-OMP/fix_nphug_omp.cpp | 461 +
src/USER-OMP/fix_nphug_omp.h | 98 +
src/USER-OMP/fix_npt_asphere_omp.cpp | 68 +
src/USER-OMP/fix_npt_asphere_omp.h | 48 +
src/USER-OMP/fix_npt_omp.cpp | 68 +
src/USER-OMP/fix_npt_omp.h | 48 +
src/USER-OMP/fix_npt_sphere_omp.cpp | 68 +
src/USER-OMP/fix_npt_sphere_omp.h | 48 +
src/USER-OMP/fix_nve_omp.cpp | 123 +
src/USER-OMP/fix_nve_omp.h | 48 +
src/USER-OMP/fix_nve_sphere_omp.cpp | 32 +-
src/USER-OMP/fix_nve_sphere_omp.h | 4 +-
src/USER-OMP/fix_nvt_asphere_omp.cpp | 49 +
src/USER-OMP/fix_nvt_asphere_omp.h | 48 +
src/USER-OMP/fix_nvt_omp.cpp | 49 +
src/USER-OMP/fix_nvt_omp.h | 48 +
src/USER-OMP/fix_nvt_sllod_omp.cpp | 141 +
src/USER-OMP/fix_nvt_sllod_omp.h | 67 +
src/USER-OMP/fix_nvt_sphere_omp.cpp | 49 +
src/USER-OMP/fix_nvt_sphere_omp.h | 48 +
src/USER-OMP/fix_omp.cpp | 193 +-
src/USER-OMP/fix_omp.h | 35 +-
src/USER-OMP/fix_peri_neigh_omp.cpp | 5 +-
src/USER-OMP/fix_peri_neigh_omp.h | 4 +-
src/USER-OMP/fix_qeq_comb_omp.cpp | 87 +-
src/USER-OMP/fix_rigid_nh_omp.cpp | 969 +
src/USER-OMP/fix_rigid_nh_omp.h | 114 +
src/USER-OMP/fix_rigid_nph_omp.cpp | 92 +
src/USER-OMP/fix_rigid_nph_omp.h | 37 +
src/USER-OMP/fix_rigid_npt_omp.cpp | 104 +
src/USER-OMP/fix_rigid_npt_omp.h | 37 +
src/USER-OMP/fix_rigid_nve_omp.cpp | 28 +
src/USER-OMP/fix_rigid_nve_omp.h | 36 +
src/USER-OMP/fix_rigid_nvt_omp.cpp | 51 +
src/USER-OMP/fix_rigid_nvt_omp.h | 36 +
src/USER-OMP/fix_rigid_omp.cpp | 673 +
src/USER-OMP/fix_rigid_omp.h | 45 +
src/USER-OMP/fix_rigid_small_omp.cpp | 620 +
src/USER-OMP/fix_rigid_small_omp.h | 134 +
src/USER-OMP/fix_shear_history_omp.cpp | 138 +-
src/USER-OMP/fix_shear_history_omp.h | 2 +-
src/USER-OMP/fix_wall_gran_omp.cpp | 87 +-
src/USER-OMP/fix_wall_gran_omp.h | 2 +-
src/USER-OMP/improper_class2_omp.cpp | 497 +-
src/USER-OMP/improper_class2_omp.h | 4 +-
src/USER-OMP/improper_cossq_omp.cpp | 268 +
src/USER-OMP/improper_cossq_omp.h | 46 +
src/USER-OMP/improper_cvff_omp.cpp | 127 +-
src/USER-OMP/improper_cvff_omp.h | 2 +-
src/USER-OMP/improper_fourier_omp.cpp | 283 +
src/USER-OMP/improper_fourier_omp.h | 53 +
src/USER-OMP/improper_harmonic_omp.cpp | 120 +-
src/USER-OMP/improper_harmonic_omp.h | 2 +-
src/USER-OMP/improper_ring_omp.cpp | 264 +
src/USER-OMP/improper_ring_omp.h | 46 +
src/USER-OMP/improper_umbrella_omp.cpp | 122 +-
src/USER-OMP/improper_umbrella_omp.h | 2 +-
src/USER-OMP/msm_cg_omp.cpp | 548 +
src/USER-OMP/msm_cg_omp.h | 141 +
src/USER-OMP/msm_omp.cpp | 465 +
src/USER-OMP/msm_omp.h | 46 +
src/USER-OMP/neigh_derive_omp.cpp | 62 +-
src/USER-OMP/neigh_full_omp.cpp | 322 +-
src/USER-OMP/neigh_gran_omp.cpp | 390 +-
src/USER-OMP/neigh_half_bin_omp.cpp | 339 +-
src/USER-OMP/neigh_half_multi_omp.cpp | 211 +-
src/USER-OMP/neigh_half_nsq_omp.cpp | 207 +-
src/USER-OMP/neigh_respa_omp.cpp | 701 +-
src/USER-OMP/neighbor_omp.h | 32 +-
src/USER-OMP/pair_adp_omp.cpp | 210 +-
src/USER-OMP/pair_adp_omp.h | 2 +-
src/USER-OMP/pair_airebo_omp.cpp | 3205 +-
src/USER-OMP/pair_airebo_omp.h | 10 +-
src/USER-OMP/pair_beck_omp.cpp | 76 +-
src/USER-OMP/pair_beck_omp.h | 2 +-
src/USER-OMP/pair_born_coul_long_omp.cpp | 124 +-
src/USER-OMP/pair_born_coul_long_omp.h | 2 +-
src/USER-OMP/pair_born_coul_msm_omp.cpp | 188 +
src/USER-OMP/pair_born_coul_msm_omp.h | 48 +
src/USER-OMP/pair_born_coul_wolf_omp.cpp | 120 +-
src/USER-OMP/pair_born_coul_wolf_omp.h | 2 +-
src/USER-OMP/pair_born_omp.cpp | 80 +-
src/USER-OMP/pair_born_omp.h | 2 +-
src/USER-OMP/pair_brownian_omp.cpp | 205 +-
src/USER-OMP/pair_brownian_omp.h | 2 +-
src/USER-OMP/pair_brownian_poly_omp.cpp | 185 +-
src/USER-OMP/pair_brownian_poly_omp.h | 2 +-
src/USER-OMP/pair_buck_coul_cut_omp.cpp | 106 +-
src/USER-OMP/pair_buck_coul_cut_omp.h | 2 +-
src/USER-OMP/pair_buck_coul_long_omp.cpp | 120 +-
src/USER-OMP/pair_buck_coul_long_omp.h | 2 +-
src/USER-OMP/pair_buck_coul_msm_omp.cpp | 188 +
src/USER-OMP/pair_buck_coul_msm_omp.h | 48 +
src/USER-OMP/pair_buck_coul_omp.cpp | 228 -
src/USER-OMP/pair_buck_coul_omp.h | 48 -
src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 1175 +
src/USER-OMP/pair_buck_long_coul_long_omp.h | 113 +
src/USER-OMP/pair_buck_omp.cpp | 84 +-
src/USER-OMP/pair_buck_omp.h | 2 +-
src/USER-OMP/pair_cdeam_omp.cpp | 404 +-
src/USER-OMP/pair_cdeam_omp.h | 4 +-
src/USER-OMP/pair_colloid_omp.cpp | 182 +-
src/USER-OMP/pair_colloid_omp.h | 2 +-
src/USER-OMP/pair_comb_omp.cpp | 282 +-
src/USER-OMP/pair_coul_cut_omp.cpp | 74 +-
src/USER-OMP/pair_coul_cut_omp.h | 2 +-
src/USER-OMP/pair_coul_debye_omp.cpp | 78 +-
src/USER-OMP/pair_coul_debye_omp.h | 2 +-
src/USER-OMP/pair_coul_diel_omp.cpp | 86 +-
src/USER-OMP/pair_coul_diel_omp.h | 2 +-
src/USER-OMP/pair_coul_dsf_omp.cpp | 177 +
src/USER-OMP/pair_coul_dsf_omp.h | 48 +
src/USER-OMP/pair_coul_long_omp.cpp | 133 +-
src/USER-OMP/pair_coul_long_omp.h | 2 +-
src/USER-OMP/pair_coul_msm_omp.cpp | 191 +
src/USER-OMP/pair_coul_msm_omp.h | 48 +
src/USER-OMP/pair_coul_wolf_omp.cpp | 102 +-
src/USER-OMP/pair_coul_wolf_omp.h | 2 +-
src/USER-OMP/pair_dipole_cut_omp.cpp | 286 -
src/USER-OMP/pair_dipole_cut_omp.h | 48 -
src/USER-OMP/pair_dipole_sf_omp.cpp | 318 -
src/USER-OMP/pair_dipole_sf_omp.h | 48 -
src/USER-OMP/pair_dpd_omp.cpp | 120 +-
src/USER-OMP/pair_dpd_omp.h | 2 +-
src/USER-OMP/pair_dpd_tstat_omp.cpp | 110 +-
src/USER-OMP/pair_dpd_tstat_omp.h | 2 +-
src/USER-OMP/pair_eam_alloy_omp.cpp | 26 +-
src/USER-OMP/pair_eam_alloy_omp.h | 2 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 30 +-
src/USER-OMP/pair_eam_fs_omp.h | 2 +-
src/USER-OMP/pair_eam_omp.cpp | 165 +-
src/USER-OMP/pair_eam_omp.h | 2 +-
src/USER-OMP/pair_edip_omp.cpp | 195 +-
src/USER-OMP/pair_eim_omp.cpp | 146 +-
src/USER-OMP/pair_eim_omp.h | 2 +-
src/USER-OMP/pair_gauss_cut_omp.cpp | 76 +-
src/USER-OMP/pair_gauss_cut_omp.h | 2 +-
src/USER-OMP/pair_gauss_omp.cpp | 87 +-
src/USER-OMP/pair_gauss_omp.h | 2 +-
src/USER-OMP/pair_gayberne_omp.cpp | 154 +-
src/USER-OMP/pair_gayberne_omp.h | 2 +-
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 254 +-
src/USER-OMP/pair_gran_hertz_history_omp.h | 2 +-
src/USER-OMP/pair_gran_hooke_history_omp.cpp | 263 +-
src/USER-OMP/pair_gran_hooke_history_omp.h | 2 +-
src/USER-OMP/pair_gran_hooke_omp.cpp | 222 +-
src/USER-OMP/pair_gran_hooke_omp.h | 2 +-
src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp | 241 +-
src/USER-OMP/pair_hbond_dreiding_lj_omp.h | 2 +-
src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp | 239 +-
src/USER-OMP/pair_hbond_dreiding_morse_omp.h | 2 +-
src/USER-OMP/pair_line_lj_omp.cpp | 342 +-
src/USER-OMP/pair_line_lj_omp.h | 2 +-
src/USER-OMP/pair_lj96_cut_omp.cpp | 83 +-
src/USER-OMP/pair_lj96_cut_omp.h | 2 +-
.../pair_lj_charmm_coul_charmm_implicit_omp.cpp | 166 +-
.../pair_lj_charmm_coul_charmm_implicit_omp.h | 2 +-
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp | 166 +-
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h | 2 +-
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp | 257 +-
src/USER-OMP/pair_lj_charmm_coul_long_omp.h | 2 +-
src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 216 +
src/USER-OMP/pair_lj_charmm_coul_msm_omp.h | 48 +
src/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp | 261 -
src/USER-OMP/pair_lj_charmm_coul_pppm_omp.h | 54 -
src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp | 116 +-
src/USER-OMP/pair_lj_class2_coul_cut_omp.h | 2 +-
src/USER-OMP/pair_lj_class2_coul_long_omp.cpp | 132 +-
src/USER-OMP/pair_lj_class2_coul_long_omp.h | 2 +-
src/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp | 228 -
src/USER-OMP/pair_lj_class2_coul_pppm_omp.h | 54 -
src/USER-OMP/pair_lj_class2_omp.cpp | 82 +-
src/USER-OMP/pair_lj_class2_omp.h | 2 +-
src/USER-OMP/pair_lj_coul_omp.cpp | 232 -
src/USER-OMP/pair_lj_coul_omp.h | 48 -
src/USER-OMP/pair_lj_cubic_omp.cpp | 90 +-
src/USER-OMP/pair_lj_cubic_omp.h | 2 +-
src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp | 114 +-
src/USER-OMP/pair_lj_cut_coul_cut_omp.h | 2 +-
src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp | 118 +-
src/USER-OMP/pair_lj_cut_coul_debye_omp.h | 2 +-
src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp | 201 +
src/USER-OMP/pair_lj_cut_coul_dsf_omp.h | 48 +
src/USER-OMP/pair_lj_cut_coul_long_omp.cpp | 169 +-
src/USER-OMP/pair_lj_cut_coul_long_omp.h | 2 +-
src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp | 485 -
src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h | 56 -
src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 210 +
src/USER-OMP/pair_lj_cut_coul_msm_omp.h | 48 +
src/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp | 246 -
src/USER-OMP/pair_lj_cut_coul_pppm_omp.h | 54 -
src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp | 507 -
src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h | 61 -
src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 286 +
src/USER-OMP/pair_lj_cut_dipole_cut_omp.h | 48 +
src/USER-OMP/pair_lj_cut_omp.cpp | 112 +-
src/USER-OMP/pair_lj_cut_omp.h | 2 +-
src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp | 467 +
src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h | 53 +
src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp | 510 +
src/USER-OMP/pair_lj_cut_tip4p_long_omp.h | 53 +
src/USER-OMP/pair_lj_expand_omp.cpp | 84 +-
src/USER-OMP/pair_lj_expand_omp.h | 4 +-
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp | 134 +-
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h | 2 +-
src/USER-OMP/pair_lj_gromacs_omp.cpp | 80 +-
src/USER-OMP/pair_lj_gromacs_omp.h | 2 +-
src/USER-OMP/pair_lj_long_coul_long_omp.cpp | 1174 +
src/USER-OMP/pair_lj_long_coul_long_omp.h | 65 +
src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp | 2019 +
src/USER-OMP/pair_lj_long_tip4p_long_omp.h | 72 +
src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp | 259 +-
src/USER-OMP/pair_lj_sdk_coul_long_omp.h | 2 +-
src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 229 +
src/USER-OMP/pair_lj_sdk_coul_msm_omp.h | 49 +
src/USER-OMP/pair_lj_sdk_omp.cpp | 122 +-
src/USER-OMP/pair_lj_sdk_omp.h | 2 +-
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 319 +
src/USER-OMP/pair_lj_sf_dipole_sf_omp.h | 48 +
src/USER-OMP/pair_lj_sf_omp.cpp | 84 +-
src/USER-OMP/pair_lj_sf_omp.h | 2 +-
src/USER-OMP/pair_lj_smooth_linear_omp.cpp | 78 +-
src/USER-OMP/pair_lj_smooth_linear_omp.h | 2 +-
src/USER-OMP/pair_lj_smooth_omp.cpp | 108 +-
src/USER-OMP/pair_lj_smooth_omp.h | 2 +-
src/USER-OMP/pair_lubricate_omp.cpp | 211 +-
src/USER-OMP/pair_lubricate_omp.h | 2 +-
src/USER-OMP/pair_lubricate_poly_omp.cpp | 227 +-
src/USER-OMP/pair_lubricate_poly_omp.h | 2 +-
src/USER-OMP/pair_meam_spline_omp.cpp | 192 +-
src/USER-OMP/pair_meam_spline_omp.h | 2 +-
src/USER-OMP/pair_morse_omp.cpp | 78 +-
src/USER-OMP/pair_morse_omp.h | 2 +-
src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 199 +
src/USER-OMP/pair_nb3b_harmonic_omp.h | 48 +
src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp | 198 +
src/USER-OMP/pair_nm_cut_coul_cut_omp.h | 48 +
src/USER-OMP/pair_nm_cut_coul_long_omp.cpp | 234 +
src/USER-OMP/pair_nm_cut_coul_long_omp.h | 48 +
src/USER-OMP/pair_nm_cut_omp.cpp | 169 +
src/USER-OMP/pair_nm_cut_omp.h | 48 +
src/USER-OMP/pair_peri_lps_omp.cpp | 91 +-
src/USER-OMP/pair_peri_lps_omp.h | 2 +-
src/USER-OMP/pair_peri_pmb_omp.cpp | 58 +-
src/USER-OMP/pair_peri_pmb_omp.h | 2 +-
src/USER-OMP/pair_rebo_omp.cpp | 2 +-
src/USER-OMP/pair_rebo_omp.h | 2 +-
src/USER-OMP/pair_resquared_omp.cpp | 68 +-
src/USER-OMP/pair_resquared_omp.h | 2 +-
src/USER-OMP/pair_soft_omp.cpp | 74 +-
src/USER-OMP/pair_soft_omp.h | 2 +-
src/USER-OMP/pair_sw_omp.cpp | 112 +-
src/USER-OMP/pair_sw_omp.h | 2 +-
src/USER-OMP/pair_table_omp.cpp | 172 +-
src/USER-OMP/pair_table_omp.h | 2 +-
src/USER-OMP/pair_tersoff_mod_omp.cpp | 250 +
src/USER-OMP/pair_tersoff_mod_omp.h | 43 +
src/USER-OMP/pair_tersoff_omp.cpp | 144 +-
src/USER-OMP/pair_tersoff_table_omp.cpp | 514 +-
src/USER-OMP/pair_tersoff_zbl_omp.cpp | 83 +-
src/USER-OMP/pair_tersoff_zbl_omp.h | 6 +-
src/USER-OMP/pair_tip4p_cut_omp.cpp | 441 +
src/USER-OMP/pair_tip4p_cut_omp.h | 53 +
src/USER-OMP/pair_tip4p_long_omp.cpp | 482 +
src/USER-OMP/pair_tip4p_long_omp.h | 53 +
src/USER-OMP/pair_tri_lj_omp.cpp | 480 +-
src/USER-OMP/pair_tri_lj_omp.h | 2 +-
src/USER-OMP/pair_yukawa_colloid_omp.cpp | 83 +-
src/USER-OMP/pair_yukawa_colloid_omp.h | 2 +-
src/USER-OMP/pair_yukawa_omp.cpp | 82 +-
src/USER-OMP/pair_yukawa_omp.h | 2 +-
src/USER-OMP/pair_zbl_omp.cpp | 170 +
src/USER-OMP/pair_zbl_omp.h | 48 +
src/USER-OMP/pppm_cg_omp.cpp | 879 +-
src/USER-OMP/pppm_cg_omp.h | 23 +-
src/USER-OMP/pppm_disp_omp.cpp | 1837 +
src/USER-OMP/pppm_disp_omp.h | 74 +
src/USER-OMP/pppm_disp_tip4p_omp.cpp | 1881 +
src/USER-OMP/pppm_disp_tip4p_omp.h | 84 +
src/USER-OMP/pppm_omp.cpp | 889 +-
src/USER-OMP/pppm_omp.h | 20 +-
src/USER-OMP/pppm_proxy.cpp | 65 -
src/USER-OMP/pppm_proxy.h | 47 -
src/USER-OMP/pppm_tip4p_omp.cpp | 866 +-
src/USER-OMP/pppm_tip4p_omp.h | 33 +-
src/USER-OMP/pppm_tip4p_proxy.cpp | 65 -
src/USER-OMP/pppm_tip4p_proxy.h | 47 -
src/USER-OMP/respa_omp.cpp | 358 +
src/USER-OMP/respa_omp.h | 111 +
src/USER-OMP/thr_data.cpp | 143 +-
src/USER-OMP/thr_data.h | 17 +-
src/USER-OMP/thr_omp.cpp | 786 +-
src/USER-OMP/thr_omp.h | 109 +-
src/USER-PHONON/Install.sh | 28 +
src/USER-PHONON/README | 20 +
src/USER-PHONON/fix_phonon.cpp | 927 +
src/USER-PHONON/fix_phonon.h | 185 +
src/USER-REAXC/Install.sh | 119 -
src/USER-REAXC/compute_spec_atom.cpp | 646 +
src/USER-REAXC/compute_spec_atom.h | 104 +
src/USER-REAXC/fix_qeq_reax.cpp | 195 +-
src/USER-REAXC/fix_qeq_reax.h | 17 +-
src/USER-REAXC/fix_reax_c.cpp | 12 +-
src/USER-REAXC/fix_reax_c.h | 6 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 350 +-
src/USER-REAXC/fix_reaxc_bonds.h | 26 +-
src/USER-REAXC/fix_reaxc_species.cpp | 979 +
src/USER-REAXC/fix_reaxc_species.h | 94 +
src/USER-REAXC/pair_reax_c.cpp | 369 +-
src/USER-REAXC/pair_reax_c.h | 22 +-
src/USER-REAXC/reaxc_allocate.cpp | 463 +-
src/USER-REAXC/reaxc_allocate.h | 14 +-
src/USER-REAXC/reaxc_basic_comm.cpp | 92 +-
src/USER-REAXC/reaxc_basic_comm.h | 10 +-
src/USER-REAXC/reaxc_bond_orders.cpp | 1022 +-
src/USER-REAXC/reaxc_bond_orders.h | 26 +-
src/USER-REAXC/reaxc_bonds.cpp | 160 +-
src/USER-REAXC/reaxc_bonds.h | 10 +-
src/USER-REAXC/reaxc_control.cpp | 63 +-
src/USER-REAXC/reaxc_control.h | 6 +-
src/USER-REAXC/reaxc_defs.h | 48 +-
src/USER-REAXC/reaxc_ffield.cpp | 606 +-
src/USER-REAXC/reaxc_ffield.h | 6 +-
src/USER-REAXC/reaxc_forces.cpp | 724 +-
src/USER-REAXC/reaxc_forces.h | 14 +-
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 282 +-
src/USER-REAXC/reaxc_hydrogen_bonds.h | 8 +-
src/USER-REAXC/reaxc_init_md.cpp | 431 +-
src/USER-REAXC/reaxc_init_md.h | 12 +-
src/USER-REAXC/reaxc_io_tools.cpp | 1152 +-
src/USER-REAXC/reaxc_io_tools.h | 108 +-
src/USER-REAXC/reaxc_list.cpp | 42 +-
src/USER-REAXC/reaxc_list.h | 6 +-
src/USER-REAXC/reaxc_lookup.cpp | 226 +-
src/USER-REAXC/reaxc_lookup.h | 10 +-
src/USER-REAXC/reaxc_multi_body.cpp | 268 +-
src/USER-REAXC/reaxc_multi_body.h | 9 +-
src/USER-REAXC/reaxc_nonbonded.cpp | 348 +-
src/USER-REAXC/reaxc_nonbonded.h | 16 +-
src/USER-REAXC/reaxc_reset_tools.cpp | 59 +-
src/USER-REAXC/reaxc_reset_tools.h | 12 +-
src/USER-REAXC/reaxc_system_props.cpp | 218 +-
src/USER-REAXC/reaxc_system_props.h | 14 +-
src/USER-REAXC/reaxc_tool_box.cpp | 95 +-
src/USER-REAXC/reaxc_tool_box.h | 6 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 846 +-
src/USER-REAXC/reaxc_torsion_angles.h | 8 +-
src/USER-REAXC/reaxc_traj.cpp | 876 +-
src/USER-REAXC/reaxc_traj.h | 14 +-
src/USER-REAXC/reaxc_types.h | 180 +-
src/USER-REAXC/reaxc_valence_angles.cpp | 792 +-
src/USER-REAXC/reaxc_valence_angles.h | 12 +-
src/USER-REAXC/reaxc_vector.cpp | 69 +-
src/USER-REAXC/reaxc_vector.h | 6 +-
src/USER-SPH/Install.sh | 59 -
src/USER-SPH/atom_vec_meso.cpp | 1481 +-
src/USER-SPH/atom_vec_meso.h | 17 +-
src/USER-SPH/compute_meso_e_atom.cpp | 6 +-
src/USER-SPH/compute_meso_e_atom.h | 2 +-
src/USER-SPH/compute_meso_rho_atom.cpp | 6 +-
src/USER-SPH/compute_meso_rho_atom.h | 2 +-
src/USER-SPH/compute_meso_t_atom.cpp | 12 +-
src/USER-SPH/compute_meso_t_atom.h | 2 +-
src/USER-SPH/fix_meso.cpp | 1 -
src/USER-SPH/fix_meso.h | 2 +-
src/USER-SPH/fix_meso_stationary.cpp | 1 -
src/USER-SPH/fix_meso_stationary.h | 2 +-
src/USER-SPH/pair_sph_heatconduction.cpp | 4 +-
src/USER-SPH/pair_sph_heatconduction.h | 2 +-
src/USER-SPH/pair_sph_idealgas.cpp | 4 +-
src/USER-SPH/pair_sph_idealgas.h | 2 +-
src/USER-SPH/pair_sph_lj.cpp | 4 +-
src/USER-SPH/pair_sph_lj.h | 2 +-
src/USER-SPH/pair_sph_rhosum.cpp | 5 +-
src/USER-SPH/pair_sph_rhosum.h | 2 +-
src/USER-SPH/pair_sph_taitwater.cpp | 8 +-
src/USER-SPH/pair_sph_taitwater.h | 2 +-
src/USER-SPH/pair_sph_taitwater_morris.cpp | 8 +-
src/USER-SPH/pair_sph_taitwater_morris.h | 2 +-
src/VORONOI/Install.sh | 60 +
src/VORONOI/Makefile.lammps | 20 +
src/VORONOI/README | 44 +
src/VORONOI/compute_voronoi_atom.cpp | 391 +
src/VORONOI/compute_voronoi_atom.h | 73 +
src/WINDOWS/LAMMPS.sln | 36 -
src/WINDOWS/LAMMPS.vcproj | 2957 -
src/WINDOWS/LAMMPS.vsmacros | Bin 182784 -> 0 bytes
src/WINDOWS/LIGGGHTS-PUBLIC.vcxproj | 1071 -
src/WINDOWS/LIGGGHTS-PUBLIC_VS2012.sln | 56 -
src/WINDOWS/README-PUBLIC_VS2012.txt | 33 -
src/WINDOWS/README.txt | 78 -
src/WINDOWS/README_VS2012.txt | 33 -
src/WINDOWS/STUBS.vcproj | 156 -
src/WINDOWS/STUBS.vcxproj | 146 -
src/WINDOWS/extra/dirent.h | 372 -
src/WINDOWS/extra/erf.h | 19 -
src/WINDOWS/extra/erf_namd.c | 345 -
src/WINDOWS/extra/fftw2/FFTW2dll.dll | Bin 263168 -> 0 bytes
src/WINDOWS/extra/fftw2/FFTW2dll.lib | Bin 22998 -> 0 bytes
src/WINDOWS/extra/fftw2/FFTW2st.lib | Bin 404572 -> 0 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.dll | Bin 481792 -> 0 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.lib | Bin 35830 -> 0 bytes
src/WINDOWS/extra/fftw2/RFFTW2st.lib | Bin 337962 -> 0 bytes
src/WINDOWS/extra/fftw2/fftw.h | 421 -
src/WINDOWS/extra/fftw2/x64/FFTW2dll.dll | Bin 228864 -> 0 bytes
src/WINDOWS/extra/fftw2/x64/FFTW2dll.lib | Bin 9588 -> 0 bytes
src/WINDOWS/extra/fftw2/x64/FFTW2st.lib | Bin 797762 -> 0 bytes
src/WINDOWS/extra/fftw2/x64/RFFTW2dll.dll | Bin 411648 -> 0 bytes
src/WINDOWS/extra/fftw2/x64/RFFTW2dll.lib | Bin 14618 -> 0 bytes
src/WINDOWS/extra/fftw2/x64/RFFTW2st.lib | Bin 668694 -> 0 bytes
src/WINDOWS/extra/inttypes.h | 305 -
src/WINDOWS/extra/sleep.cpp | 10 -
src/WINDOWS/extra/sleep.h | 1 -
src/WINDOWS/extra/stdint.h | 247 -
src/WINDOWS/extra/sys/time.h | 28 -
src/WINDOWS/extra/unistd.h | 1 -
src/WINDOWS/settings/style_angle.h | 9 -
src/WINDOWS/settings/style_atom.h | 15 -
src/WINDOWS/settings/style_bond.h | 10 -
src/WINDOWS/settings/style_command.h | 16 -
src/WINDOWS/settings/style_compute.h | 46 -
src/WINDOWS/settings/style_dihedral.h | 7 -
src/WINDOWS/settings/style_dump.h | 13 -
src/WINDOWS/settings/style_fix.h | 118 -
src/WINDOWS/settings/style_improper.h | 5 -
src/WINDOWS/settings/style_integrate.h | 4 -
src/WINDOWS/settings/style_kspace.h | 5 -
src/WINDOWS/settings/style_minimize.h | 6 -
src/WINDOWS/settings/style_pair.h | 60 -
src/WINDOWS/settings/style_region.h | 11 -
src/XTC/Install.sh | 21 -
src/XTC/dump_xtc.cpp | 512 +-
src/XTC/dump_xtc.h | 9 +-
src/XTC/xdr_compat.cpp | 232 +-
src/XTC/xdr_compat.h | 99 +-
src/accelerator_omp.h | 55 +-
src/angle.cpp | 11 +-
src/angle.h | 7 +
src/angle_hybrid.cpp | 369 +
src/angle_hybrid.h | 95 +
src/associative_pointer_array.h | 14 +-
src/associative_pointer_array_I.h | 14 +-
src/atom.cpp | 542 +-
src/atom.h | 72 +-
src/atom_map.cpp | 304 +
src/atom_masks.h | 87 +
src/atom_vec.cpp | 272 +-
src/atom_vec.h | 51 +-
src/atom_vec_atomic.cpp | 137 +-
src/atom_vec_atomic.h | 9 +-
src/atom_vec_body.cpp | 1596 +
src/atom_vec_body.h | 155 +
src/atom_vec_charge.cpp | 158 +-
src/atom_vec_charge.h | 11 +-
src/atom_vec_ellipsoid.cpp | 285 +-
src/atom_vec_ellipsoid.h | 15 +-
src/atom_vec_hybrid.cpp | 285 +-
src/atom_vec_hybrid.h | 31 +-
src/atom_vec_line.cpp | 298 +-
src/atom_vec_line.h | 15 +-
src/atom_vec_sph.cpp | 170 +-
src/atom_vec_sph.h | 12 +-
src/atom_vec_sph_var.cpp | 188 +-
src/atom_vec_sph_var.h | 12 +-
src/atom_vec_sphere.cpp | 221 +-
src/atom_vec_sphere.h | 15 +-
src/atom_vec_tri.cpp | 322 +-
src/atom_vec_tri.h | 15 +-
src/body.cpp | 36 +
src/body.h | 62 +
src/bond.cpp | 13 +-
src/bond.h | 8 +-
src/bond_hybrid.cpp | 9 +-
src/bond_hybrid.h | 4 +-
src/cfd_datacoupling.cpp | 32 +-
src/cfd_datacoupling.h | 16 +-
src/cfd_datacoupling_file.cpp | 32 +-
src/cfd_datacoupling_file.h | 26 +-
src/cfd_datacoupling_mpi.cpp | 4 +-
src/cfd_datacoupling_mpi.h | 12 +-
src/cfd_regionmodel.h | 9 +-
src/cfd_regionmodel_none.cpp | 6 +-
src/change_box.cpp | 130 +-
src/change_box.h | 10 +-
src/citeme.cpp | 75 +
src/citeme.h | 41 +
src/cohesion_model_sjkr.h | 102 +
src/cohesion_model_sjkr2.h | 103 +
src/comm.cpp | 350 +-
src/comm.h | 24 +-
src/comm_I.h | 27 +
src/compute.cpp | 9 +-
src/compute.h | 5 +
src/compute_angle_local.cpp | 6 +-
src/compute_atom_molecule.cpp | 17 +-
src/compute_bond_local.cpp | 60 +-
src/compute_bond_local.h | 2 +
src/compute_centro_atom.cpp | 2 +-
src/compute_cluster_atom.cpp | 5 +-
src/compute_cna_atom.cpp | 2 +-
src/compute_com_molecule.cpp | 18 +-
src/compute_contact_atom.h | 4 +
src/compute_coord_atom.cpp | 148 +-
src/compute_coord_atom.h | 11 +-
src/compute_dihedral_local.cpp | 6 +-
src/compute_displace_atom.cpp | 59 +-
src/compute_displace_atom.h | 2 +-
src/compute_erotate_rigid.cpp | 74 +
src/compute_erotate_rigid.h | 56 +
src/compute_erotate_sphere.cpp | 18 +-
src/compute_erotate_sphere.h | 12 +-
src/compute_erotate_sphere_atom.cpp | 125 +
src/compute_erotate_sphere_atom.h | 73 +
src/compute_group_group.cpp | 228 +-
src/compute_group_group.h | 19 +-
src/compute_gyration.cpp | 66 +-
src/compute_gyration.h | 3 +-
src/compute_gyration_molecule.cpp | 179 +-
src/compute_gyration_molecule.h | 7 +-
src/compute_improper_local.cpp | 6 +-
src/compute_inertia_molecule.cpp | 184 +
src/compute_inertia_molecule.h | 65 +
src/compute_ke_rigid.cpp | 73 +
src/compute_ke_rigid.h | 52 +
src/compute_msd.cpp | 89 +-
src/compute_msd.h | 11 +-
src/compute_msd_molecule.cpp | 24 +-
src/compute_nparticles_tracer_region.cpp | 8 +-
src/compute_pair_gran_local.cpp | 8 +-
src/compute_pe_atom.cpp | 16 +-
src/compute_property_atom.cpp | 261 +-
src/compute_property_atom.h | 7 +-
src/compute_property_local.cpp | 146 +-
src/compute_property_local.h | 2 +
src/compute_rdf.cpp | 2 +-
src/compute_reduce.cpp | 13 +-
src/compute_slice.cpp | 7 +-
src/compute_stress_atom.cpp | 34 +-
src/compute_temp.cpp | 2 +-
src/compute_temp.h | 3 +-
src/compute_temp_com.cpp | 13 +-
src/compute_temp_com.h | 4 +-
src/compute_temp_deform.cpp | 20 +-
src/compute_temp_deform.h | 6 +-
src/compute_temp_partial.cpp | 4 +-
src/compute_temp_partial.h | 3 +-
src/compute_temp_profile.cpp | 306 +-
src/compute_temp_profile.h | 5 +-
src/compute_temp_ramp.cpp | 7 +-
src/compute_temp_ramp.h | 5 +-
src/compute_temp_region.cpp | 7 +-
src/compute_temp_region.h | 1 +
src/compute_temp_sphere.cpp | 15 +-
src/compute_temp_sphere.h | 1 +
src/compute_ti.cpp | 178 -
src/compute_ti.h | 82 -
src/compute_vacf.cpp | 139 +
src/compute_vacf.h | 57 +
src/contact_interface.h | 143 +
src/contact_model_constants.h | 64 +
src/contact_models.h | 268 +
src/container_base.cpp | 20 +-
src/container_base.h | 12 +-
src/container_base_I.h | 2 +-
src/create_atoms.cpp | 204 +-
src/create_atoms.h | 11 +
src/create_box.cpp | 14 +-
src/custom_value_tracker.cpp | 4 +-
src/custom_value_tracker.h | 24 +-
src/custom_value_tracker_I.h | 20 +-
src/delete_atoms.cpp | 73 +-
src/delete_atoms.h | 9 +-
src/delete_bonds.cpp | 69 +-
src/dihedral.cpp | 11 +-
src/dihedral.h | 7 +
src/dihedral_hybrid.cpp | 350 +
src/dihedral_hybrid.h | 85 +
src/displace_atoms.cpp | 116 +-
src/displace_atoms.h | 14 +-
src/domain.cpp | 452 +-
src/domain.h | 107 +-
src/dump.cpp | 283 +-
src/dump.h | 44 +-
src/dump_atom.cpp | 141 +-
src/dump_atom.h | 16 +-
src/dump_atom_vtk.cpp | 10 +-
src/dump_cfg.cpp | 174 +-
src/dump_cfg.h | 4 +-
src/dump_custom.cpp | 242 +-
src/dump_custom.h | 20 +-
src/dump_dcd.cpp | 26 +-
src/dump_dcd.h | 5 +-
src/dump_image.cpp | 145 +-
src/dump_image.h | 19 +-
src/dump_local.cpp | 79 +-
src/dump_local.h | 6 +
src/dump_mesh_stl.cpp | 6 +
src/dump_mesh_vtk.cpp | 32 +
src/dump_movie.cpp | 106 +
src/dump_movie.h | 73 +
src/dump_xyz.cpp | 129 +-
src/dump_xyz.h | 17 +-
src/error.cpp | 17 +-
src/error.h | 1 +
src/finish.cpp | 99 +-
src/fix.cpp | 24 +-
src/fix.h | 91 +-
src/fix_adapt.cpp | 27 +-
src/fix_adapt.h | 5 +
src/fix_addforce.cpp | 15 +-
src/fix_ave_atom.cpp | 30 +-
src/fix_ave_atom.h | 8 +-
src/fix_ave_correlate.cpp | 38 +-
src/fix_ave_correlate.h | 9 +-
src/fix_ave_euler.cpp | 4 +-
src/fix_ave_histo.cpp | 115 +-
src/fix_ave_histo.h | 9 +-
src/fix_ave_spatial.cpp | 93 +-
src/fix_ave_spatial.h | 21 +-
src/fix_ave_time.cpp | 44 +-
src/fix_ave_time.h | 9 +-
src/fix_aveforce.cpp | 19 +-
src/fix_box_relax.cpp | 118 +-
src/fix_box_relax.h | 19 +-
src/fix_cfd_coupling.cpp | 6 +-
src/fix_cfd_coupling.h | 6 +-
src/fix_cfd_coupling_force_implicit.cpp | 39 +-
src/fix_check_timestep_gran.cpp | 22 +-
src/fix_check_timestep_gran.h | 3 +-
src/fix_contact_history.cpp | 658 +-
src/fix_contact_history.h | 97 +-
src/fix_contact_history_I.h | 171 -
src/fix_contact_history_mesh.cpp | 558 +
src/fix_contact_history_mesh.h | 136 +
src/fix_contact_history_mesh_I.h | 212 +
src/fix_deform.cpp | 83 +-
src/fix_deform.h | 10 +-
src/fix_deposit.cpp | 74 +-
src/fix_deposit.h | 15 +-
src/fix_drag.cpp | 12 +-
src/fix_dt_reset.cpp | 36 +-
src/fix_dt_reset.h | 14 +-
src/fix_dummy.h | 4 +-
src/fix_efield.cpp | 231 -
src/fix_efield.h | 75 -
src/fix_evaporate.cpp | 386 -
src/fix_external.cpp | 150 +-
src/fix_external.h | 17 +-
src/fix_gravity.cpp | 18 +-
src/fix_heat.cpp | 246 +-
src/fix_heat.h | 20 +
src/fix_heat_gran.cpp | 3 +-
src/fix_heat_gran.h | 2 +-
src/fix_indent.cpp | 30 +-
src/fix_indent.h | 10 +-
src/fix_insert.cpp | 8 +-
src/fix_insert.h | 3 +
src/fix_insert_stream.cpp | 44 +-
src/fix_insert_stream.h | 7 +-
src/fix_langevin.cpp | 666 +-
src/fix_langevin.h | 42 +-
src/fix_lineforce.cpp | 7 +-
src/fix_massflow_mesh.cpp | 19 +-
src/fix_mesh.cpp | 13 +-
src/fix_mesh_surface.cpp | 54 +-
src/fix_mesh_surface.h | 17 +-
src/fix_mesh_surface_stress.cpp | 6 +-
src/fix_mesh_surface_stress_servo.cpp | 631 +-
src/fix_mesh_surface_stress_servo.h | 42 +-
src/fix_minimize.cpp | 2 +-
src/fix_minimize.h | 2 +-
src/fix_momentum.cpp | 29 +-
src/fix_move.cpp | 65 +-
src/fix_move.h | 14 +-
src/fix_move_mesh.cpp | 3 +-
src/fix_neighlist_mesh.cpp | 274 +-
src/fix_neighlist_mesh.h | 59 +-
src/fix_nh.cpp | 199 +-
src/fix_nh.h | 22 +-
src/fix_nve_limit.cpp | 13 +-
src/fix_orient_fcc.cpp | 592 -
src/fix_planeforce.cpp | 7 +-
src/fix_press_berendsen.cpp | 35 +-
src/fix_print.cpp | 26 +-
src/fix_print.h | 1 +
src/fix_property_atom.cpp | 59 +-
src/fix_property_atom.h | 8 +-
src/fix_property_atom_tracer.cpp | 8 +
src/fix_property_global.cpp | 34 +-
src/fix_property_global.h | 1 +
src/fix_read_restart.cpp | 7 +-
src/fix_read_restart.h | 2 +-
src/fix_recenter.cpp | 10 +-
src/fix_recenter.h | 10 +-
src/fix_respa.cpp | 5 +-
src/fix_respa.h | 3 +-
src/fix_restrain.cpp | 687 +-
src/fix_restrain.h | 28 +-
src/fix_rigid.cpp | 2753 +-
src/fix_rigid.h | 97 +-
src/fix_rigid_nh.cpp | 1430 +
src/fix_rigid_nh.h | 183 +
src/fix_rigid_nph.cpp | 90 +
src/fix_rigid_nph.h | 48 +
src/fix_rigid_npt.cpp | 100 +
src/fix_rigid_npt.h | 62 +
src/fix_rigid_nve.cpp | 259 +-
src/fix_rigid_nve.h | 17 +-
src/fix_rigid_nvt.cpp | 690 +-
src/fix_rigid_nvt.h | 58 +-
src/fix_rigid_small.cpp | 3139 +
src/fix_rigid_small.h | 248 +
src/fix_scalar_transport_equation.cpp | 10 +-
src/fix_setforce.cpp | 7 +-
src/fix_shake.cpp | 304 +-
src/fix_shake.h | 15 +-
src/fix_shear_history.cpp | 241 +-
src/fix_shear_history.h | 16 +-
src/fix_sph_density_corr.cpp | 23 +-
src/fix_sph_density_corr.h | 2 +-
src/fix_sph_pressure.cpp | 26 +-
src/fix_spring.cpp | 22 +-
src/fix_spring_rg.cpp | 23 +-
src/fix_spring_self.cpp | 42 +-
src/fix_spring_self.h | 2 +-
src/fix_store.cpp | 191 +
src/fix_store.h | 62 +
src/fix_store_state.cpp | 129 +-
src/fix_store_state.h | 2 +-
src/fix_temp_berendsen.cpp | 76 +-
src/fix_temp_berendsen.h | 19 +-
src/fix_temp_rescale.cpp | 72 +-
src/fix_temp_rescale.h | 19 +-
src/fix_thermal_conductivity.cpp | 328 -
src/fix_tmd.cpp | 86 +-
src/fix_tmd.h | 11 +-
src/fix_ttm.cpp | 685 -
src/fix_viscosity.cpp | 307 -
src/fix_viscous.cpp | 8 +-
src/fix_wall.cpp | 153 +-
src/fix_wall.h | 38 +-
src/fix_wall_gran.cpp | 237 +-
src/fix_wall_gran.h | 29 +-
src/fix_wall_gran_base.h | 168 +
src/fix_wall_gran_hertz_history.cpp | 132 -
src/fix_wall_gran_hertz_history.h | 53 -
src/fix_wall_gran_hertz_history_simple.cpp | 79 -
src/fix_wall_gran_hertz_history_simple.h | 52 -
src/fix_wall_gran_hooke.cpp | 187 -
src/fix_wall_gran_hooke.h | 54 -
src/fix_wall_gran_hooke_history.cpp | 595 -
src/fix_wall_gran_hooke_history.h | 84 -
src/fix_wall_gran_hooke_history_simple.cpp | 132 -
src/fix_wall_gran_hooke_history_simple.h | 56 -
src/fix_wall_gran_hooke_simple.cpp | 129 -
src/fix_wall_gran_hooke_simple.h | 56 -
src/fix_wall_lj1043.cpp | 81 +
src/fix_wall_lj1043.h | 42 +
src/fix_wall_reflect.cpp | 14 +-
src/fix_wall_reflect.h | 10 +-
src/fix_wall_region.cpp | 7 +-
src/fix_wall_region_sph.cpp | 4 +-
src/fix_wall_sph.cpp | 18 +-
src/force.cpp | 358 +-
src/force.h | 63 +-
src/general_container.h | 5 +
src/general_container_I.h | 6 +-
src/global_properties.cpp | 535 +
src/global_properties.h | 81 +
src/group.cpp | 367 +-
src/group.h | 8 +
src/image.cpp | 541 +-
src/image.h | 65 +-
src/improper.cpp | 11 +-
src/improper.h | 7 +
src/improper_hybrid.cpp | 338 +
src/improper_hybrid.h | 84 +
src/input.cpp | 425 +-
src/input.h | 56 +-
src/input_mesh_tet.cpp | 46 +-
src/input_mesh_tet.h | 2 +-
src/input_mesh_tri.cpp | 87 +-
src/input_multisphere.cpp | 44 +-
src/integrate.cpp | 2 +
src/kspace.cpp | 305 +-
src/kspace.h | 156 +-
src/lammps.cpp | 289 +-
src/lammps.h | 14 +-
src/lattice.cpp | 52 +-
src/lattice.h | 2 +-
src/library.cpp | 205 +-
src/library.h | 16 +-
src/library_cfd_coupling.cpp | 12 +-
src/lmptype.h | 20 +-
src/lmpwindows.h | 21 +-
src/math_complex.h | 72 +
src/math_extra.h | 50 +-
src/math_special.h | 66 +
src/math_vector.h | 448 +
src/memory.h | 4 +
src/mesh_mover.h | 94 +-
src/min.cpp | 27 +-
src/min_fire.cpp | 6 +-
src/min_fire.h | 4 +-
src/min_linesearch.cpp | 2 +-
src/min_quickmin.cpp | 2 +-
src/min_quickmin.h | 1 +
src/minimize.cpp | 9 +-
src/modify.cpp | 492 +-
src/modify.h | 53 +-
src/modify_liggghts.cpp | 18 +-
src/multi_node_mesh.h | 7 +-
src/multi_node_mesh_parallel_buffer_I.h | 16 +-
src/multi_vector_container.h | 11 +-
src/my_page.h | 232 +
src/my_pool_chunk.h | 205 +
src/neigh_bond.cpp | 159 +
src/neigh_bond.h | 25 +-
src/neigh_derive.cpp | 171 +-
src/neigh_full.cpp | 125 +-
src/neigh_gran.cpp | 177 +-
src/neigh_half_bin.cpp | 204 +-
src/neigh_half_multi.cpp | 76 +-
src/neigh_half_nsq.cpp | 157 +-
src/neigh_list.cpp | 82 +-
src/neigh_list.h | 14 +-
src/neigh_request.cpp | 25 +-
src/neigh_request.h | 21 +-
src/neigh_respa.cpp | 349 +-
src/neigh_stencil.cpp | 47 +-
src/neighbor.cpp | 321 +-
src/neighbor.h | 47 +-
src/normal_model_hertz.h | 132 +
src/normal_model_hertz_stiffness.h | 131 +
src/normal_model_hooke.h | 170 +
src/normal_model_hooke_hysteresis.h | 184 +
src/normal_model_hooke_stiffness.h | 148 +
src/os_specific.h | 66 +
src/output.cpp | 414 +-
src/output.h | 46 +-
src/pair.cpp | 635 +-
src/pair.h | 58 +-
src/pair_beck.cpp | 25 +-
src/pair_born.cpp | 45 +-
src/pair_born.h | 2 +
src/pair_born_coul_wolf.cpp | 54 +-
src/pair_born_coul_wolf.h | 7 +-
src/pair_buck.cpp | 40 +-
src/pair_buck.h | 2 +
src/pair_buck_coul_cut.cpp | 47 +-
src/pair_buck_coul_cut.h | 2 +
src/pair_coul_cut.cpp | 7 +-
src/pair_coul_debye.cpp | 4 +-
src/pair_coul_dsf.cpp | 335 +
src/pair_coul_dsf.h | 72 +
src/pair_coul_wolf.cpp | 9 +-
src/pair_coul_wolf.h | 5 +-
src/pair_dpd.cpp | 34 +-
src/pair_dpd.h | 6 +-
src/pair_dpd_tstat.cpp | 87 +-
src/pair_dpd_tstat.h | 4 +
src/pair_gauss.cpp | 36 +-
src/pair_gran.cpp | 91 +-
src/pair_gran.h | 49 +-
src/pair_gran_base.h | 268 +
src/pair_gran_hertz_history.cpp | 87 -
src/pair_gran_hertz_history.h | 53 -
src/pair_gran_hertz_history_simple.cpp | 108 -
src/pair_gran_hertz_history_simple.h | 58 -
src/pair_gran_hooke.h | 53 -
src/pair_gran_hooke_history.h | 103 -
src/pair_gran_hooke_history_hysteresis.cpp | 542 -
src/pair_gran_hooke_history_hysteresis.h | 71 -
src/pair_gran_hooke_history_simple.cpp | 207 -
src/pair_gran_hooke_history_simple.h | 60 -
src/pair_gran_hooke_simple.cpp | 208 -
src/pair_gran_hooke_simple.h | 60 -
src/pair_hybrid.cpp | 124 +-
src/pair_hybrid.h | 9 +-
src/pair_hybrid_overlay.cpp | 2 +-
src/pair_lj96_cut.cpp | 36 +-
src/pair_lj96_cut.h | 2 +
src/pair_lj_cubic.cpp | 4 +-
src/pair_lj_cut.cpp | 34 +-
src/pair_lj_cut.h | 2 +
src/pair_lj_cut_coul_cut.cpp | 55 +-
src/pair_lj_cut_coul_cut.h | 5 +-
src/pair_lj_cut_coul_debye.cpp | 6 +-
src/pair_lj_cut_coul_dsf.cpp | 473 +
src/pair_lj_cut_coul_dsf.h | 77 +
src/pair_lj_expand.cpp | 52 +-
src/pair_lj_expand.h | 3 +
src/pair_lj_gromacs.cpp | 39 +-
src/pair_lj_gromacs.h | 2 +
src/pair_lj_gromacs_coul_gromacs.cpp | 41 +-
src/pair_lj_gromacs_coul_gromacs.h | 2 +
src/pair_lj_smooth.cpp | 39 +-
src/pair_lj_smooth.h | 2 +
src/pair_lj_smooth_linear.cpp | 13 +-
src/pair_mie_cut.cpp | 743 +
src/pair_mie_cut.h | 81 +
src/pair_morse.cpp | 37 +-
src/pair_morse.h | 2 +
src/pair_soft.cpp | 35 +-
src/pair_soft.h | 2 +
src/pair_sph.cpp | 10 +-
src/pair_sph_artvisc_tenscorr.cpp | 12 +-
src/pair_table.cpp | 69 +-
src/pair_table.h | 3 +-
src/pair_yukawa.cpp | 34 +-
src/pair_yukawa.h | 2 +
src/pair_zbl.cpp | 435 +
src/pair_zbl.h | 84 +
src/pointers.h | 4 +-
src/primitive_wall_definitions.h | 2 +-
src/property_registry.cpp | 171 +
src/property_registry.h | 153 +
src/random_mars.cpp | 1 +
src/random_park.cpp | 2 +
src/read_data.cpp | 573 +-
src/read_data.h | 40 +-
src/read_dump.cpp | 944 +
src/read_dump.h | 155 +
src/read_restart.cpp | 13 +-
src/reader.cpp | 75 +
src/reader.h | 61 +
src/reader_native.cpp | 330 +
src/reader_native.h | 66 +
src/reader_xyz.cpp | 215 +
src/reader_xyz.h | 66 +
src/region.cpp | 54 +-
src/region.h | 25 +-
src/region_block.cpp | 13 +-
src/region_cone.cpp | 37 +-
src/region_cylinder.cpp | 87 +-
src/region_cylinder.h | 19 +
src/region_intersect.cpp | 60 +-
src/region_intersect.h | 3 +
src/region_plane.cpp | 19 +-
src/region_prism.cpp | 18 +-
src/region_sphere.cpp | 62 +-
src/region_sphere.h | 18 +
src/region_union.cpp | 62 +-
src/region_union.h | 3 +
src/replicate.cpp | 22 +-
src/rerun.cpp | 192 +
src/rerun.h | 55 +
src/respa.cpp | 166 +-
src/respa.h | 29 +-
src/rolling_model_cdt.h | 135 +
src/rolling_model_epsd.h | 206 +
src/rolling_model_epsd2.h | 181 +
src/run.cpp | 3 +-
src/scalar_container.h | 11 +-
src/set.cpp | 408 +-
src/set.h | 10 +-
src/settings.h | 239 +
src/special.cpp | 749 +-
src/special.h | 21 +-
src/sph_kernel_cubicspline.h | 4 +-
src/sph_kernel_cubicspline2D.h | 4 +-
src/sph_kernel_spiky.h | 4 +-
src/sph_kernel_spiky2D.h | 4 +-
src/sph_kernel_wendland.h | 4 +-
src/sph_kernel_wendland2D.h | 4 +-
src/style_angle.h | 1 +
src/style_atom.h | 3 +-
doc/fix_wall_region_sph.html => src/style_body.h | 0
src/style_cohesion_model.h | 2 +
src/style_command.h | 4 +
src/style_compute.h | 14 +-
.../style_contact_model.blacklist | 0
src/style_contact_model.h | 120 +
src/style_dihedral.h | 1 +
src/style_dump.h | 1 +
src/style_fix.h | 28 +-
src/style_improper.h | 1 +
src/style_normal_model.h | 5 +
src/style_pair.h | 21 +-
src/style_reader.h | 2 +
src/style_rolling_model.h | 3 +
src/style_sph_kernel.h | 6 +-
src/style_surface_model.h | 1 +
src/style_tangential_model.h | 2 +
src/surface_model_default.h | 121 +
src/tangential_model_history.h | 172 +
src/tangential_model_no_history.h | 118 +
src/thermo.cpp | 179 +-
src/thermo.h | 17 +-
src/timer.cpp | 5 +
src/timer.h | 2 +-
src/tri_mesh_I.h | 8 +-
src/universe.cpp | 8 +-
src/universe.h | 4 +-
src/update.cpp | 115 +-
src/update.h | 23 +-
src/variable.cpp | 1036 +-
src/variable.h | 78 +-
src/vector_container.h | 11 +-
src/velocity.cpp | 129 +-
src/velocity.h | 12 +-
src/verlet.cpp | 21 +-
src/version.h | 2 +-
src/version_liggghts.h | 4 +
src/version_liggghts.txt | 4 +
src/write_data.cpp | 691 +
src/write_data.h | 76 +
src/write_dump.cpp | 83 +
src/write_dump.h | 55 +
src/write_restart.cpp | 18 +-
tools/Makefile | 3 -
tools/README | 4 +-
tools/amber2lmp/README | 8 +
tools/amber2lmp/amber2lammps.py | 16 +
tools/binary2txt.cpp | 25 +-
tools/ch2lmp/example/1ac7_trj.psf | 1 -
tools/eff/lmp2xyz.py | 19 +-
tools/kate/README.txt | 6 +
tools/kate/lammps.xml | 878 +
tools/moltemplate/LICENSE.TXT | 28 +
tools/moltemplate/README.TXT | 61 +
tools/moltemplate/common/amber/README.TXT | 27 +
tools/moltemplate/common/amber/amberparm2lt.sh | 193 +
.../common/amber/amberparm_angle_to_lt.py | 50 +
.../common/amber/amberparm_bond_to_lt.py | 47 +
.../common/amber/amberparm_dihedral_to_lt.py | 157 +
.../common/amber/amberparm_improper_to_lt.py | 62 +
.../common/amber/amberparm_mass_to_lt.py | 19 +
.../common/amber/amberparm_pair_to_lt.py | 20 +
tools/moltemplate/common/gaff.lt | 11383 ++
tools/moltemplate/common/graphene.lt | 106 +
.../common/images/graphene_unit_cell.jpg | Bin 0 -> 13144 bytes
.../common/images/ice_rect8_unitcell.png | Bin 0 -> 21951 bytes
.../common/images/spce_ball_and_stick.jpg | Bin 0 -> 5644 bytes
tools/moltemplate/common/spce.lt | 52 +
tools/moltemplate/common/spce_ice_rect8.lt | 57 +
tools/moltemplate/common/tip3p_1983.lt | 123 +
tools/moltemplate/common/tip3p_2004.lt | 97 +
tools/moltemplate/common/trappe1998.lt | 50 +
tools/moltemplate/common/watmw.lt | 54 +
.../CG_biomolecules/membrane+protein/README.TXT | 70 +
.../CG_biomolecules/membrane+protein/README_run.sh | 33 +
.../membrane+protein/README_setup.sh | 28 +
.../membrane+protein/README_visualize.txt | 87 +
.../images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg | Bin 0 -> 85276 bytes
.../images/membrane+protein_t=0ps_LR.jpg | Bin 0 -> 71073 bytes
.../images/membrane+protein_t=0ps_no_pbc_LR.jpg | Bin 0 -> 51659 bytes
.../images/membrane+protein_t=0ps_top_LR.jpg | Bin 0 -> 67085 bytes
.../images/membrane+protein_t=5000ps_LR.jpg | Bin 0 -> 71011 bytes
.../moltemplate_files/1beadProtSci2010.lt | 254 +
.../1beadProtSci2010_variations.lt | 225 +
.../moltemplate_files/CGLipidBr2005.lt | 198 +
.../calc_table/calc_CGLipidTableINTvsINT.py | 34 +
.../calc_table/version_charmm_cutoff/calc_table.py | 70 +
.../membrane+protein/moltemplate_files/system.lt | 207 +
.../moltemplate_files/table_int.dat | 1139 +
.../CG_biomolecules/membrane+protein/run.in.min | 35 +
.../CG_biomolecules/membrane+protein/run.in.npt | 60 +
.../CG_biomolecules/membrane+protein/run.in.nvt | 67 +
.../membrane_BranniganPRE2005/README.TXT | 33 +
.../membrane_BranniganPRE2005/README_run.sh | 33 +
.../membrane_BranniganPRE2005/README_setup.sh | 28 +
.../membrane_BranniganPRE2005/README_visualize.txt | 87 +
.../membrane_BranniganPRE2005/images/DLPC.jpg | Bin 0 -> 4915 bytes
.../images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg | Bin 0 -> 58412 bytes
.../DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg | Bin 0 -> 36618 bytes
.../images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg | Bin 0 -> 62029 bytes
.../membrane_BranniganPRE2005/images/DPPC.jpg | Bin 0 -> 5834 bytes
.../moltemplate_files/CGLipidBr2005Orig.lt | 191 +
.../moltemplate_files/calc_table/calc_table.py | 34 +
.../calc_table/version_charmm_cutoff/calc_table.py | 70 +
.../moltemplate_files/system.lt | 94 +
.../moltemplate_files/table_int.dat | 1139 +
.../membrane_BranniganPRE2005/run.in.min | 28 +
.../membrane_BranniganPRE2005/run.in.npt | 57 +
.../membrane_BranniganPRE2005/run.in.nvt | 53 +
.../1bead+chaperone/README.TXT | 33 +
.../frustrated+chaperonin/README.TXT | 32 +
.../frustrated+chaperonin/README_run.sh | 31 +
.../frustrated+chaperonin/README_setup.sh | 24 +
.../frustrated+chaperonin/README_visualize.txt | 87 +
.../psf_file_created_by_topotools/system.psf | 86 +
.../images/misfolded+chaperonin_t=0tau_LR.jpg | Bin 0 -> 15784 bytes
.../images/unfolded+chaperonin_t=508750tau_LR.jpg | Bin 0 -> 17080 bytes
.../moltemplate_files/1beadFrustrated.lt | 216 +
.../moltemplate_files/1beadFrustrated_variants.lt | 85 +
.../moltemplate_files/chaperonin.lt | 41 +
.../generate_tables/calc_chaperone_table.py | 87 +
.../generate_tables/calc_dihedral_table.py | 67 +
.../moltemplate_files/system.lt | 45 +
.../moltemplate_files/table_chaperonin_h=0.475.dat | 1188 +
.../moltemplate_files/table_chaperonin_h=0.dat | 1187 +
.../table_dihedral_frustrated.dat | 735 +
.../frustrated+chaperonin/run.in.min | 25 +
.../frustrated+chaperonin/run.in.nvt | 48 +
.../frustrated+minichaperone/README.TXT | 38 +
.../frustrated+minichaperone/README_run.sh | 31 +
.../frustrated+minichaperone/README_setup.sh | 24 +
.../frustrated+minichaperone/README_visualize.txt | 87 +
.../psf_file_created_by_topotools/system.psf | 476 +
.../protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg | Bin 0 -> 31162 bytes
...tein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg | Bin 0 -> 26258 bytes
.../moltemplate_files/1beadFrustrated.lt | 216 +
.../moltemplate_files/1beadFrustrated_variants.lt | 85 +
.../generate_tables/calc_chaperone_table.py | 87 +
.../generate_tables/calc_dihedral_table.py | 67 +
.../moltemplate_files/minichaperone.lt | 41 +
.../moltemplate_files/system.lt | 72 +
.../table_dihedral_frustrated.dat | 735 +
.../table_minichaperone_h=0.6.dat | 988 +
.../moltemplate_files/table_minichaperone_h=0.dat | 989 +
.../frustrated+minichaperone/run.in.min | 24 +
.../frustrated+minichaperone/run.in.nvt | 46 +
.../1bead+chaperone/frustrated/README.TXT | 29 +
.../1bead+chaperone/frustrated/README_run.sh | 21 +
.../1bead+chaperone/frustrated/README_setup.sh | 24 +
.../frustrated/README_visualize.txt | 87 +
.../psf_file_created_by_topotools/system.psf | 85 +
.../images/initial_conformation_t=0tau.jpg | Bin 0 -> 23358 bytes
.../images/misfolded_conformation_t=1250tau.jpg | Bin 0 -> 23090 bytes
.../moltemplate_files/1beadFrustrated.lt | 216 +
.../moltemplate_files/1beadFrustrated_variants.lt | 85 +
.../generate_tables/calc_dihedral_table.py | 67 +
.../frustrated/moltemplate_files/system.lt | 20 +
.../table_dihedral_frustrated.dat | 735 +
.../1bead+chaperone/frustrated/run.in.min | 19 +
.../frustrated/run_short_sim.in.nvt | 50 +
.../unfrustrated+chaperonin/README.TXT | 32 +
.../unfrustrated+chaperonin/README_run.sh | 31 +
.../unfrustrated+chaperonin/README_setup.sh | 24 +
.../unfrustrated+chaperonin/README_visualize.txt | 87 +
.../psf_file_created_by_topotools/system.psf | 98 +
.../images/unfrustrated+chaperonin_t=0tau_LR.jpg | Bin 0 -> 16267 bytes
.../images/unfrustrated+chaperonin_t=105tau_LR.jpg | Bin 0 -> 14944 bytes
.../moltemplate_files/1beadUnfrustrated.lt | 255 +
.../1beadUnfrustrated_variants.lt | 45 +
.../moltemplate_files/chaperonin.lt | 41 +
.../generate_tables/calc_chaperone_table.py | 87 +
.../moltemplate_files/system.lt | 45 +
.../moltemplate_files/table_chaperonin_h=0.475.dat | 1188 +
.../moltemplate_files/table_chaperonin_h=0.dat | 1187 +
.../unfrustrated+chaperonin/run.in.min | 19 +
.../unfrustrated+chaperonin/run.in.nvt | 48 +
.../1bead+chaperone/unfrustrated/README.TXT | 27 +
.../1bead+chaperone/unfrustrated/README_run.sh | 31 +
.../1bead+chaperone/unfrustrated/README_setup.sh | 23 +
.../unfrustrated/README_visualize.txt | 87 +
.../psf_file_created_by_topotools/system.psf | 97 +
.../unfrustrated/images/unfrustrated_t=0tau_LR.jpg | Bin 0 -> 7690 bytes
.../images/unfrustrated_t=200tau_LR.jpg | Bin 0 -> 7821 bytes
.../moltemplate_files/1beadUnfrustrated.lt | 255 +
.../1beadUnfrustrated_variants.lt | 45 +
.../unfrustrated/moltemplate_files/system.lt | 11 +
.../1bead+chaperone/unfrustrated/run.in.min | 19 +
.../1bead+chaperone/unfrustrated/run.in.nvt | 46 +
.../1beadProtSci2010/README.TXT | 44 +
.../1beadProtSci2010/README_run.sh | 31 +
.../1beadProtSci2010/README_setup.sh | 23 +
.../1beadProtSci2010/README_visualize.txt | 87 +
.../1beadProtSci2010/images/4HelixBundle_t=0.jpg | Bin 0 -> 38619 bytes
.../1beadProtSci2010/images/4SheetBundle_t=0.jpg | Bin 0 -> 49905 bytes
.../psf_file_created_by_topotools/system.psf | 214 +
.../moltemplate_files/1beadProtSci2010.lt | 274 +
.../1beadProtSci2010/moltemplate_files/README.sh | 13 +
.../other_implementations/README.TXT | 13 +
.../charmm/1beadProtSci2010.lt | 411 +
.../class2/1beadProtSci2010.lt | 385 +
.../1beadProtSci2010/moltemplate_files/system.lt | 25 +
.../1beadProtSci2010/run.in.min | 19 +
.../1beadProtSci2010/run.in.nvt | 44 +
.../vesicle_Brannigan2005+Bellesia2010/README.TXT | 114 +
.../README_run.sh | 24 +
.../README_setup.sh | 50 +
.../README_visualize.txt | 87 +
.../images/vesicle_membrane+protein_L.jpg | Bin 0 -> 284201 bytes
.../moltemplate_files/1beadProtSci2010.lt | 233 +
.../1beadProtSci2010_variations.lt | 225 +
.../moltemplate_files/CGLipidBr2005.lt | 198 +
.../moltemplate_files/README.sh | 22 +
.../calc_table/calc_CGLipidTableINTvsINT.py | 34 +
.../calc_table/version_charmm_cutoff/calc_table.py | 70 +
.../moltemplate_files/system.lt | 192 +
.../moltemplate_files/table_int.dat | 1139 +
.../packmol_files/DLPC.xyz | 6 +
.../packmol_files/DPPC.xyz | 7 +
.../packmol_files/README.sh | 23 +
.../packmol_files/protein.xyz | 75 +
.../packmol_files/step1_proteins.inp | 49 +
.../packmol_files/step2_innerlayer.inp | 70 +
.../packmol_files/step3_outerlayer.inp | 70 +
.../vesicle_Brannigan2005+Bellesia2010/run.in.min | 53 +
.../vesicle_Brannigan2005+Bellesia2010/run.in.nvt | 70 +
.../CG_misc/2bead_heteropolymer/README.TXT | 17 +
.../CG_misc/2bead_heteropolymer/README_run.sh | 20 +
.../CG_misc/2bead_heteropolymer/README_setup.sh | 23 +
.../2bead_heteropolymer/README_visualize.txt | 86 +
.../images/2bead_heteropolymer_t=0.jpg | Bin 0 -> 76183 bytes
.../images/2bead_heteropolymer_t=1000ps.jpg | Bin 0 -> 54472 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 +
.../CG_misc/random_heteropolymer/README_run.sh | 14 +
.../CG_misc/random_heteropolymer/README_setup.sh | 23 +
.../random_heteropolymer/README_visualize.txt | 87 +
.../CG_misc/random_heteropolymer/images/2bead.jpg | Bin 0 -> 2713 bytes
.../CG_misc/random_heteropolymer/images/3bead.jpg | Bin 0 -> 4410 bytes
.../psf_file_created_by_topotools/system.psf | 277 +
.../images/random_heteropolymer_t=0ps.jpg | Bin 0 -> 31115 bytes
.../images/random_heteropolymer_t=1ns.jpg | Bin 0 -> 29582 bytes
.../moltemplate_files/monomers.lt | 115 +
.../moltemplate_files/polymer.lt | 82 +
.../moltemplate_files/system.lt | 33 +
.../CG_misc/random_heteropolymer/run.in.nvt | 29 +
.../examples/CG_misc/translocation/README.TXT | 23 +
.../examples/CG_misc/translocation/README_run.sh | 28 +
.../examples/CG_misc/translocation/README_setup.sh | 23 +
.../CG_misc/translocation/README_visualize.txt | 87 +
.../CG_misc/translocation/images/polymer_LR.jpg | Bin 0 -> 5568 bytes
.../CG_misc/translocation/images/solvent_LR.jpg | Bin 0 -> 23407 bytes
.../images/walls+solvent+polymer_t=0.jpg | Bin 0 -> 105467 bytes
.../CG_misc/translocation/images/walls_LR.jpg | Bin 0 -> 13280 bytes
.../translocation/moltemplate_files/monomer.lt | 111 +
.../translocation/moltemplate_files/polymer.lt | 35 +
.../translocation/moltemplate_files/solvent.lt | 23 +
.../moltemplate_files/solvent_single.lt | 22 +
.../translocation/moltemplate_files/system.lt | 55 +
.../translocation/moltemplate_files/wall_single.lt | 21 +
.../translocation/moltemplate_files/walls.lt | 23 +
.../examples/CG_misc/translocation/run.in.npt | 70 +
.../examples/CG_misc/translocation/run.in.nvt | 43 +
.../CG_solvent/cyclododecane+watMW/README.TXT | 28 +
.../CG_solvent/cyclododecane+watMW/README_run.sh | 31 +
.../CG_solvent/cyclododecane+watMW/README_setup.sh | 25 +
.../cyclododecane+watMW/README_visualize.txt | 87 +
.../images/cyclododecane+watMW_t=0ps_LR.jpg | Bin 0 -> 51874 bytes
.../images/cyclododecane+watMW_t=400ps_LR.jpg | Bin 0 -> 39434 bytes
.../images/cyclododecane+watMW_t=50ps_LR.jpg | Bin 0 -> 39341 bytes
.../cyclododecane+watMW/images/cyclopentane.jpg | Bin 0 -> 12330 bytes
.../images/cyclopentane_unrelaxed.jpg | Bin 0 -> 12835 bytes
.../psf_file_created_by_topotools/system.psf | 3669 +
.../cyclododecane+watMW/images/watMW.jpg | Bin 0 -> 3141 bytes
.../moltemplate_files/README.sh | 11 +
.../moltemplate_files/cyclododecane.lt | 55 +
.../moltemplate_files/system.lt | 62 +
.../moltemplate_files/trappe1998.lt | 50 +
.../version_more_comments/system.lt | 80 +
.../cyclododecane+watMW/moltemplate_files/watmw.lt | 54 +
.../CG_solvent/cyclododecane+watMW/run.in.npt | 58 +
.../CG_solvent/cyclododecane+watMW/run.in.nvt | 78 +
tools/moltemplate/examples/README.TXT | 24 +
.../waterTIP3P+isobutane/README.TXT | 42 +
.../waterTIP3P+isobutane/README_run.sh | 39 +
.../waterTIP3P+isobutane/README_setup.sh | 89 +
.../waterTIP3P+isobutane/README_visualize.txt | 87 +
.../waterTIP3P+isobutane/images/isobutane.jpg | Bin 0 -> 24301 bytes
.../images/water+isobutane_t=0_LR.jpg | Bin 0 -> 104035 bytes
.../images/water+isobutane_t=840ps_LR.jpg | Bin 0 -> 73375 bytes
.../waterTIP3P+isobutane/images/water.jpg | Bin 0 -> 10076 bytes
.../moltemplate_files/isobutane.lt | 51 +
.../moltemplate_files/system.lt | 31 +
.../waterTIP3P+isobutane/run.in.npt | 37 +
.../waterTIP3P+isobutane/run.in.nvt | 53 +
.../aluminum_crystal_strain/README.TXT | 54 +
.../aluminum_crystal_strain/README_setup.sh | 29 +
.../aluminum_crystal_strain/README_visualize.txt | 87 +
.../aluminum_crystal_strain/images/AlCell_LR.jpg | Bin 0 -> 2364 bytes
.../images/AlCrystal10x10x10_t=0steps_LR.jpg | Bin 0 -> 30158 bytes
.../images/AlCrystal10x10x10_t=20000steps_LR.jpg | Bin 0 -> 29910 bytes
.../moltemplate_files/README.sh | 22 +
.../moltemplate_files/al_cell.lt | 64 +
.../moltemplate_files/system.lt | 35 +
.../aluminum_crystal_strain/run.in | 76 +
.../cnad-cnt/README_FIRST.TXT | 83 +
.../cnad-cnt/README_step1_run_ltemplify.sh | 13 +
.../cnad-cnt/README_step2_run_moltemplate.sh | 18 +
.../cnad-cnt/README_step3_run_lammps.sh | 16 +
.../cnad-cnt/README_visualize.txt | 50 +
.../cnad-cnt/cnad-cnt.data | 1157 +
.../cnad-cnt/cnad-cnt.in | 49 +
.../cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg | Bin 0 -> 29386 bytes
.../cnad-cnt/images/cnad-cnt_orig.jpg | Bin 0 -> 19144 bytes
.../cnad-cnt/images/cnad.jpg | Bin 0 -> 18403 bytes
.../cnad-cnt/images/cnt.jpg | Bin 0 -> 20633 bytes
.../cnad-cnt_after_rotate_and_copy.psf | 598 +
.../cnad-cnt_orig.psf | 489 +
.../cnad-cnt/run.in.nvt | 46 +
.../cnad-cnt/system.lt | 29 +
.../all_atom_examples/ice_crystal/README_run.sh | 33 +
.../all_atom_examples/ice_crystal/README_setup.sh | 23 +
.../ice_crystal/README_visualize.txt | 87 +
.../images/ice_rect8_crystal_3x2x2_LR.jpg | Bin 0 -> 25820 bytes
.../ice_crystal/moltemplate_files/spce.lt | 52 +
.../moltemplate_files/spce_ice_rect8.lt | 57 +
.../ice_crystal/moltemplate_files/system.lt | 11 +
.../all_atom_examples/ice_crystal/run.in.npt | 38 +
.../all_atom_examples/ice_crystal/run.in.nvt | 61 +
.../all_atom_examples/nanotube+water/README.TXT | 51 +
.../all_atom_examples/nanotube+water/README_run.sh | 24 +
.../nanotube+water/README_setup.sh | 23 +
.../nanotube+water/README_visualize.txt | 77 +
.../psf_file_created_by_topotools/system.psf | 3195 +
.../nanotube+water/images/graphene_unit_cell.jpg | Bin 0 -> 13144 bytes
.../nanotube+walls+water_side_pbc_t=0ps_LR.jpg | Bin 0 -> 30772 bytes
.../nanotube+walls+water_side_pbc_t=108ps_LR.jpg | Bin 0 -> 28367 bytes
.../nanotube+walls+water_side_pbc_t=305ps_LR.jpg | Bin 0 -> 27305 bytes
.../nanotube+walls+water_top_nopbc_t=0_LR.jpg | Bin 0 -> 33740 bytes
.../images/nanotube+walls_side_nopbc_LR.jpg | Bin 0 -> 18748 bytes
.../nanotube+water/images/water_side_nopbc_LR.jpg | Bin 0 -> 26968 bytes
.../nanotube+water/moltemplate_files/README.sh | 27 +
.../nanotube+water/moltemplate_files/graphene.lt | 119 +
.../moltemplate_files/graphene_walls.lt | 54 +
.../nanotube+water/moltemplate_files/nanotube.lt | 24 +
.../nanotube+water/moltemplate_files/spce.lt | 52 +
.../nanotube+water/moltemplate_files/system.lt | 46 +
.../nanotube+water/moltemplate_files/water_box.lt | 20 +
.../all_atom_examples/nanotube+water/run.in.npt | 98 +
.../all_atom_examples/nanotube+water/run.in.nvt | 71 +
.../waterSPCE_from_PDBfile/README.TXT | 10 +
.../waterSPCE_from_PDBfile/README_run.sh | 31 +
.../waterSPCE_from_PDBfile/README_setup.sh | 32 +
.../waterSPCE_from_PDBfile/README_visualize.txt | 64 +
.../waterSPCE_from_PDBfile/moltemplate_files/.0 | 0
.../moltemplate_files/README.sh | 11 +
.../moltemplate_files/solvate.pdb | 782 +
.../moltemplate_files/spce.lt | 52 +
.../moltemplate_files/system.lt | 16 +
.../waterSPCE_from_PDBfile/run.in.npt | 52 +
.../waterSPCE_from_PDBfile/run.in.nvt | 67 +
.../waterSPCE+Na+Cl/README_run.sh | 33 +
.../waterSPCE+Na+Cl/README_setup.sh | 23 +
.../waterSPCE+Na+Cl/README_visualize.txt | 87 +
.../waterSPCE+Na+Cl/images/Cl.jpg | Bin 0 -> 1577 bytes
.../waterSPCE+Na+Cl/images/Na.jpg | Bin 0 -> 1595 bytes
.../psf_file_created_by_topotools/system.psf | 4257 +
.../waterSPCE+Na+Cl/images/wat.jpg | Bin 0 -> 5644 bytes
.../waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg | Bin 0 -> 169027 bytes
.../images/waterSPCE+Na+Cl_t=100ps.jpg | Bin 0 -> 144377 bytes
.../waterSPCE+Na+Cl/moltemplate_files/ions.lt | 60 +
.../waterSPCE+Na+Cl/moltemplate_files/spce.lt | 52 +
.../waterSPCE+Na+Cl/moltemplate_files/system.lt | 52 +
.../all_atom_examples/waterSPCE+Na+Cl/run.in.npt | 44 +
.../all_atom_examples/waterSPCE+Na+Cl/run.in.nvt | 61 +
.../examples/silly/pyramids_vs_gravity/README.TXT | 22 +
.../pyramids_vs_gravity/README_VMD_graphene.txt | 28 +
.../silly/pyramids_vs_gravity/README_setup.sh | 23 +
.../silly/pyramids_vs_gravity/README_visualize.txt | 76 +
.../images/pyramids_vs_gravity_t=04800steps_LR.jpg | Bin 0 -> 88094 bytes
.../images/pyramids_vs_gravity_t=12200steps_LR.jpg | Bin 0 -> 91240 bytes
.../images/pyramids_vs_gravity_t=33000steps_LR.jpg | Bin 0 -> 98828 bytes
.../moltemplate_files/README.sh | 15 +
.../moltemplate_files/graphene.lt | 61 +
.../moltemplate_files/graphene_wall.lt | 21 +
.../moltemplate_files/pyramids.lt | 283 +
.../moltemplate_files/system.lt | 80 +
.../examples/silly/pyramids_vs_gravity/run.in | 64 +
.../examples/silly/sierpinski/README.TXT | 45 +
.../examples/silly/sierpinski/README_setup.sh | 29 +
.../examples/silly/sierpinski/README_visualize.txt | 87 +
.../examples/silly/sierpinski/images/AlCell_LR.jpg | Bin 0 -> 2364 bytes
.../examples/silly/sierpinski/images/lvl1_LR.jpg | Bin 0 -> 2623 bytes
.../examples/silly/sierpinski/images/lvl2_LR.jpg | Bin 0 -> 7722 bytes
.../examples/silly/sierpinski/images/lvl3_LR.jpg | Bin 0 -> 16455 bytes
...serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg | Bin 0 -> 82092 bytes
.../serpinski_cube_lattice_8cells_t=7400_LR.jpg | Bin 0 -> 21718 bytes
.../silly/sierpinski/moltemplate_files/al_cell.lt | 64 +
.../elegant_inefficient_version/al_cell.lt | 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/examples/silly/sierpinski/run.in | 38 +
tools/moltemplate/moltemplate_manual.pdf | Bin 0 -> 697917 bytes
tools/moltemplate/src/bonds_by_type.py | 379 +
tools/moltemplate/src/dump2data.py | 1263 +
tools/moltemplate/src/extract_lammps_data.py | 119 +
tools/moltemplate/src/ltemplify.py | 2236 +
tools/moltemplate/src/lttree.py | 745 +
tools/moltemplate/src/lttree_check.py | 2211 +
tools/moltemplate/src/lttree_postprocess.py | 335 +
tools/moltemplate/src/lttree_styles.py | 239 +
tools/moltemplate/src/moltemplate.sh | 1775 +
tools/moltemplate/src/nbody_Angles.py | 41 +
tools/moltemplate/src/nbody_Bonds.py | 31 +
tools/moltemplate/src/nbody_Dihedrals.py | 44 +
tools/moltemplate/src/nbody_Impropers.py | 49 +
.../nbody_Dihedrals_nosym.py | 32 +
.../nbody_ImpropersIJIKILnoswap.py | 33 +
.../nbody_ImpropersIJIKILswapJK.py | 49 +
.../nbody_ImpropersIJIKILswapJKL.py | 43 +
.../nbody_ImpropersJIJKJLnoswap.py | 32 +
.../nbody_ImpropersJIJKJLswapIK.py | 47 +
.../nbody_ImpropersJIJKJLswapIKL.py | 44 +
.../nbody_ImpropersJIJKJLswapJK.py | 48 +
tools/moltemplate/src/nbody_by_type.py | 639 +
tools/moltemplate/src/nbody_by_type_lib.py | 383 +
tools/moltemplate/src/nbody_by_type_lib_old.py | 312 +
.../moltemplate/src/nbody_fix_ttree_assignments.py | 149 +
tools/moltemplate/src/nbody_graph_search.py | 976 +
tools/moltemplate/src/nbody_reorder_atoms.py | 74 +
tools/moltemplate/src/ordereddict.py | 258 +
tools/moltemplate/src/pdbsort.py | 138 +
tools/moltemplate/src/postprocess_input_script.py | 146 +
tools/moltemplate/src/raw2data.py | 99 +
tools/moltemplate/src/remove_duplicate_atoms.py | 53 +
tools/moltemplate/src/remove_duplicates_nbody.py | 49 +
.../moltemplate/src/renumber_DATA_first_column.py | 69 +
tools/moltemplate/src/ttree.py | 4762 +
tools/moltemplate/src/ttree_lex.py | 2090 +
tools/moltemplate/src/ttree_matrix_stack.py | 618 +
tools/moltemplate/src/ttree_render.py | 115 +
tools/msi2lmp/README | 141 +-
tools/msi2lmp/TriclinicModification.pdf | Bin 78328 -> 0 bytes
tools/msi2lmp/biosym_frc_files/README | 5 -
tools/msi2lmp/biosym_frc_files/pcff.frc | 5581 -
tools/msi2lmp/frc_files/README | 10 +
.../{biosym_frc_files => frc_files}/cff91.frc | 0
.../{biosym_frc_files => frc_files}/clayff.frc | 0
tools/msi2lmp/frc_files/compass_published.frc | 1381 +
.../{biosym_frc_files => frc_files}/cvff.frc | 0
.../{biosym_frc_files => frc_files}/cvff_aug.frc | 0
tools/msi2lmp/frc_files/oplsaa.frc | 236 +
tools/msi2lmp/frc_files/pcff.frc | 5593 +
.../{biosym_frc_files => frc_files}/pcff.rlb | 0
.../pcff_templates.dat | 0
tools/msi2lmp/src/CheckLists.c | 38 +-
tools/msi2lmp/src/Forcefield.h | 52 +-
tools/msi2lmp/src/GetParameters.c | 1268 +-
tools/msi2lmp/src/InitializeItems.c | 239 +-
tools/msi2lmp/src/MakeLists.c | 509 +-
tools/msi2lmp/src/Makefile | 21 +-
tools/msi2lmp/src/Msi2LMP2.h | 213 -
tools/msi2lmp/src/ReadCarFile.c | 515 +-
tools/msi2lmp/src/ReadFrcFile.c | 172 +-
tools/msi2lmp/src/ReadMdfFile.c | 646 +-
tools/msi2lmp/src/SearchAndFill.c | 388 +-
tools/msi2lmp/src/WriteDataFile.c | 690 +-
tools/msi2lmp/src/WriteDataFile01.c | 332 -
tools/msi2lmp/src/WriteDataFile05.c | 352 -
tools/msi2lmp/src/msi2lmp.c | 492 +-
tools/msi2lmp/src/msi2lmp.h | 222 +
tools/msi2lmp/test/PyAC_bulk-clayff.car | 1287 +
tools/msi2lmp/test/PyAC_bulk-clayff.mdf | 1308 +
tools/msi2lmp/test/benzene-class1.car | 19 +
tools/msi2lmp/test/benzene-class1.mdf | 40 +
tools/msi2lmp/test/benzene-class2a.car | 19 +
tools/msi2lmp/test/benzene-class2a.mdf | 40 +
tools/msi2lmp/test/benzene-class2b.car | 19 +
tools/msi2lmp/test/benzene-class2b.mdf | 40 +
tools/msi2lmp/test/correct/data.crambin | 4727 -
tools/msi2lmp/test/correct/data.nylon | 898 -
tools/msi2lmp/test/correct/data.phen3_cff97 | 442 -
.../test/{crambin.car => crambin-class1.car} | 0
.../test/{crambin.mdf => crambin-class1.mdf} | 0
tools/msi2lmp/test/data-compare.pl | 942 +
tools/msi2lmp/test/ethane-class1.car | 15 +
tools/msi2lmp/test/ethane-class1.mdf | 36 +
tools/msi2lmp/test/ethane-class2a.car | 15 +
tools/msi2lmp/test/ethane-class2a.mdf | 36 +
tools/msi2lmp/test/ethane-class2b.car | 15 +
tools/msi2lmp/test/ethane-class2b.mdf | 36 +
tools/msi2lmp/test/ethane-oplsaa.car | 15 +
tools/msi2lmp/test/ethane-oplsaa.mdf | 36 +
tools/msi2lmp/test/h2-h2o-class1.car | 13 +
tools/msi2lmp/test/h2-h2o-class1.mdf | 33 +
tools/msi2lmp/test/h2-h2o-class2b.car | 13 +
tools/msi2lmp/test/h2-h2o-class2b.mdf | 33 +
tools/msi2lmp/test/hap_crystal-class1.car | 95 +
tools/msi2lmp/test/hap_crystal-class1.mdf | 116 +
tools/msi2lmp/test/hap_crystal-class2b.car | 95 +
tools/msi2lmp/test/hap_crystal-class2b.mdf | 116 +
tools/msi2lmp/test/hydrogen-class1.car | 9 +
tools/msi2lmp/test/hydrogen-class1.mdf | 30 +
tools/msi2lmp/test/hydrogen-class2a.car | 9 +
tools/msi2lmp/test/hydrogen-class2a.mdf | 30 +
tools/msi2lmp/test/in.PyAC_bulk-clayff | 15 +
tools/msi2lmp/test/in.benzene-class1 | 15 +
tools/msi2lmp/test/in.benzene-class2a | 15 +
tools/msi2lmp/test/in.benzene-class2b | 15 +
tools/msi2lmp/test/in.crambin-class1 | 16 +
tools/msi2lmp/test/in.ethane-class1 | 14 +
tools/msi2lmp/test/in.ethane-class2a | 15 +
tools/msi2lmp/test/in.ethane-class2b | 15 +
tools/msi2lmp/test/in.ethane-oplsaa | 14 +
tools/msi2lmp/test/in.h2-h2o-class1 | 13 +
tools/msi2lmp/test/in.h2-h2o-class2b | 13 +
tools/msi2lmp/test/in.hap_crystal-class1 | 13 +
tools/msi2lmp/test/in.hap_crystal-class2b | 14 +
tools/msi2lmp/test/in.hydrogen-class1 | 12 +
tools/msi2lmp/test/in.hydrogen-class2a | 12 +
tools/msi2lmp/test/in.naphthalene-class1 | 15 +
tools/msi2lmp/test/in.naphthalene-class2a | 15 +
tools/msi2lmp/test/in.naphthalene-class2b | 15 +
tools/msi2lmp/test/in.nylon-class1 | 16 +
tools/msi2lmp/test/in.phen3_cff97-class1 | 16 +
tools/msi2lmp/test/in.water-class1 | 13 +
tools/msi2lmp/test/in.water-class2b | 13 +
tools/msi2lmp/test/naphthalene-class1.car | 25 +
tools/msi2lmp/test/naphthalene-class1.mdf | 46 +
tools/msi2lmp/test/naphthalene-class2a.car | 25 +
tools/msi2lmp/test/naphthalene-class2a.mdf | 46 +
tools/msi2lmp/test/naphthalene-class2b.car | 25 +
tools/msi2lmp/test/naphthalene-class2b.mdf | 46 +
tools/msi2lmp/test/{nylon.car => nylon-class1.car} | 0
tools/msi2lmp/test/{nylon.mdf => nylon-class1.mdf} | 0
.../{phen3_cff97.car => phen3_cff97-class1.car} | 0
.../{phen3_cff97.mdf => phen3_cff97-class1.mdf} | 0
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 1450 +
.../msi2lmp/test/reference/PyAC_bulk-clayff.data2 | 2728 +
tools/msi2lmp/test/reference/benzene-class1.data | 135 +
tools/msi2lmp/test/reference/benzene-class1.data2 | 148 +
tools/msi2lmp/test/reference/benzene-class1.data3 | 135 +
tools/msi2lmp/test/reference/benzene-class2a.data | 179 +
tools/msi2lmp/test/reference/benzene-class2a.data2 | 192 +
tools/msi2lmp/test/reference/benzene-class2b.data | 179 +
tools/msi2lmp/test/reference/benzene-class2b.data2 | 192 +
tools/msi2lmp/test/reference/crambin-class1.data | 4727 +
tools/msi2lmp/test/reference/crambin-class1.data2 | 5370 +
tools/msi2lmp/test/reference/ethane-class1.data | 89 +
tools/msi2lmp/test/reference/ethane-class1.data2 | 97 +
tools/msi2lmp/test/reference/ethane-class2a.data | 141 +
tools/msi2lmp/test/reference/ethane-class2a.data2 | 150 +
tools/msi2lmp/test/reference/ethane-class2b.data | 141 +
tools/msi2lmp/test/reference/ethane-class2b.data2 | 150 +
tools/msi2lmp/test/reference/ethane-oplsaa.data | 89 +
tools/msi2lmp/test/reference/ethane-oplsaa.data2 | 97 +
tools/msi2lmp/test/reference/h2-h2o-class1.data | 55 +
tools/msi2lmp/test/reference/h2-h2o-class1.data2 | 59 +
tools/msi2lmp/test/reference/h2-h2o-class2b.data | 63 +
tools/msi2lmp/test/reference/h2-h2o-class2b.data2 | 67 +
.../msi2lmp/test/reference/hap_crystal-class1.data | 260 +
.../test/reference/hap_crystal-class1.data2 | 347 +
.../test/reference/hap_crystal-class2b.data | 328 +
.../test/reference/hap_crystal-class2b.data2 | 416 +
tools/msi2lmp/test/reference/hydrogen-class1.data | 36 +
tools/msi2lmp/test/reference/hydrogen-class1.data2 | 36 +
tools/msi2lmp/test/reference/hydrogen-class2a.data | 36 +
.../msi2lmp/test/reference/hydrogen-class2a.data2 | 36 +
.../msi2lmp/test/reference/naphthalene-class1.data | 185 +
.../test/reference/naphthalene-class1.data2 | 204 +
.../test/reference/naphthalene-class2a.data | 230 +
.../test/reference/naphthalene-class2a.data2 | 249 +
.../test/reference/naphthalene-class2b.data | 230 +
.../test/reference/naphthalene-class2b.data2 | 249 +
tools/msi2lmp/test/reference/nylon-class1.data | 898 +
tools/msi2lmp/test/reference/nylon-class1.data2 | 1016 +
.../msi2lmp/test/reference/phen3_cff97-class1.data | 258 +
.../test/reference/phen3_cff97-class1.data2 | 282 +
tools/msi2lmp/test/reference/water-class1.data | 49 +
tools/msi2lmp/test/reference/water-class1.data2 | 51 +
tools/msi2lmp/test/reference/water-class2b.data | 57 +
tools/msi2lmp/test/reference/water-class2b.data2 | 59 +
tools/msi2lmp/test/runtests.sh | 158 +
tools/msi2lmp/test/water-class1.car | 10 +
tools/msi2lmp/test/water-class1.mdf | 31 +
tools/msi2lmp/test/water-class2b.car | 10 +
tools/msi2lmp/test/water-class2b.mdf | 31 +
tools/phonon/Makefile | 64 +
tools/phonon/README | 31 +
tools/phonon/dynmat.cpp | 602 +
tools/phonon/dynmat.h | 66 +
tools/phonon/green.cpp | 250 +
tools/phonon/green.h | 25 +
tools/phonon/interpolate.cpp | 310 +
tools/phonon/interpolate.h | 43 +
tools/phonon/main.cpp | 18 +
tools/phonon/memory.cpp | 51 +
tools/phonon/memory.h | 430 +
tools/phonon/phonon.cpp | 1266 +
tools/phonon/phonon.h | 59 +
tools/phonon/timer.cpp | 41 +
tools/phonon/timer.h | 24 +
tools/phonon/version.h | 1 +
tools/polybond/Manual.pdf | Bin 0 -> 92552 bytes
tools/polybond/README | 12 +
tools/polybond/lmpsdata.py | 1945 +
tools/pymol_asphere/src/Makefile | 2 +-
tools/python/dump2cfg.py | 2 +-
tools/python/dump2pdb.py | 2 +-
tools/python/dump2xyz.py | 2 +-
tools/python/dumpsort.py | 2 +-
tools/python/log2txt.py | 2 +-
tools/python/logplot.py | 2 +-
tools/python/neb_combine.py | 2 +-
tools/python/neb_final.py | 2 +-
tools/restart2data.cpp | 0
tools/thermo_extract.c | 238 -
tools/xmgrace/README | 16 +
tools/xmgrace/lammpsplot.cpp | 830 +
tools/xmgrace/lammpsplot.pdf | Bin 0 -> 71715 bytes
tools/xmgrace/logplotawk.oneliner | 7 +
tools/xmgrace/logplotgrep.oneliner | 6 +
tools/xmgrace/plotthermodata.awk | 18 +
4869 files changed, 1015039 insertions(+), 219634 deletions(-)
mode change 100755 => 100644 README
create mode 100755 bench/log.30Jul13.chain.fixed.linux.1
create mode 100755 bench/log.30Jul13.chain.fixed.linux.4
create mode 100755 bench/log.30Jul13.chain.scaled.linux.4
create mode 100755 bench/log.30Jul13.chute.fixed.linux.1
create mode 100755 bench/log.30Jul13.chute.fixed.linux.4
create mode 100755 bench/log.30Jul13.chute.scaled.linux.4
create mode 100755 bench/log.30Jul13.eam.fixed.linux.1
create mode 100755 bench/log.30Jul13.eam.fixed.linux.4
create mode 100755 bench/log.30Jul13.eam.scaled.linux.4
create mode 100755 bench/log.30Jul13.lj.fixed.linux.1
create mode 100755 bench/log.30Jul13.lj.fixed.linux.4
create mode 100755 bench/log.30Jul13.lj.scaled.linux.4
create mode 100755 bench/log.30Jul13.rhodo.fixed.linux.1
create mode 100755 bench/log.30Jul13.rhodo.fixed.linux.4
create mode 100755 bench/log.30Jul13.rhodo.scaled.linux.4
delete mode 100755 bench/log.9Jan12.chain.fixed.linux.1
delete mode 100755 bench/log.9Jan12.chain.fixed.linux.4
delete mode 100755 bench/log.9Jan12.chain.scaled.linux.4
delete mode 100755 bench/log.9Jan12.chute.fixed.linux.1
delete mode 100755 bench/log.9Jan12.chute.fixed.linux.4
delete mode 100755 bench/log.9Jan12.chute.scaled.linux.4
delete mode 100755 bench/log.9Jan12.eam.fixed.linux.1
delete mode 100755 bench/log.9Jan12.eam.fixed.linux.4
delete mode 100755 bench/log.9Jan12.eam.scaled.linux.4
delete mode 100755 bench/log.9Jan12.lj.fixed.linux.1
delete mode 100755 bench/log.9Jan12.lj.fixed.linux.4
delete mode 100755 bench/log.9Jan12.lj.scaled.linux.4
delete mode 100755 bench/log.9Jan12.rhodo.fixed.linux.1
delete mode 100755 bench/log.9Jan12.rhodo.fixed.linux.4
delete mode 100755 bench/log.9Jan12.rhodo.scaled.linux.4
delete mode 100755 couple/README
delete mode 100755 couple/fortran/README
delete mode 100755 couple/fortran/libfwrapper.c
delete mode 100755 couple/lammps_quest/Makefile.g++
delete mode 100755 couple/lammps_quest/README
delete mode 100755 couple/lammps_quest/in.lammps
delete mode 100755 couple/lammps_quest/lmpqst.cpp
delete mode 100755 couple/lammps_spparks/README
delete mode 100755 couple/lammps_spparks/image.lammps.1.png
delete mode 100755 couple/lammps_spparks/image.lammps.10.png
delete mode 100755 couple/lammps_spparks/image.lammps.20.png
delete mode 100755 couple/lammps_spparks/image.spparks.1.png
delete mode 100755 couple/lammps_spparks/image.spparks.10.png
delete mode 100755 couple/lammps_spparks/image.spparks.20.png
delete mode 100755 couple/simple/README
delete mode 100755 couple/simple/in.lj
delete mode 100755 couple/simple/simple.c
delete mode 100755 couple/simple/simple.cpp
delete mode 100755 couple/simple/simple.f90
rename debian/{libliggghts2.install => libliggghts3.install} (100%)
create mode 100644 doc/Developer.pdf
create mode 100644 doc/Eqs/angle_fourier.jpg
create mode 100644 doc/Eqs/angle_fourier.tex
create mode 100644 doc/Eqs/angle_fourier_simple.jpg
create mode 100644 doc/Eqs/angle_fourier_simple.tex
create mode 100644 doc/Eqs/angle_quartic.jpg
create mode 100644 doc/Eqs/angle_quartic.tex
create mode 100644 doc/Eqs/compute_msd_nongauss.jpg
create mode 100644 doc/Eqs/compute_msd_nongauss.tex
create mode 100644 doc/Eqs/dihedral_fourier.jpg
create mode 100644 doc/Eqs/dihedral_fourier.tex
create mode 100644 doc/Eqs/dihedral_nharmonic.jpg
create mode 100644 doc/Eqs/dihedral_nharmonic.tex
create mode 100644 doc/Eqs/dihedral_quadratic.jpg
create mode 100644 doc/Eqs/dihedral_quadratic.tex
create mode 100644 doc/Eqs/dihedral_sign.jpg
create mode 100644 doc/Eqs/eff_ECP1.jpg
create mode 100644 doc/Eqs/eff_ECP1.tex
create mode 100644 doc/Eqs/eff_ECP2.jpg
create mode 100644 doc/Eqs/eff_ECP2.tex
create mode 100644 doc/Eqs/fix_gld1.jpg
create mode 100644 doc/Eqs/fix_gld1.tex
create mode 100644 doc/Eqs/fix_lb_fluid_boltzmann.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_boltzmann.tex
create mode 100644 doc/Eqs/fix_lb_fluid_fluidforce.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_fluidforce.tex
create mode 100644 doc/Eqs/fix_lb_fluid_gammadefault.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_gammadefault.tex
create mode 100644 doc/Eqs/fix_lb_fluid_navierstokes.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_navierstokes.tex
create mode 100644 doc/Eqs/fix_lb_fluid_properties.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_properties.tex
create mode 100644 doc/Eqs/fix_lb_fluid_stress.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_stress.tex
create mode 100644 doc/Eqs/fix_lb_fluid_viscosity.jpg
create mode 100755 doc/Eqs/fix_lb_fluid_viscosity.tex
create mode 100644 doc/Eqs/fix_ti_rs_force.jpg
create mode 100644 doc/Eqs/fix_ti_rs_force.tex
create mode 100644 doc/Eqs/fix_ti_rs_function_1.jpg
create mode 100644 doc/Eqs/fix_ti_rs_function_1.tex
create mode 100644 doc/Eqs/fix_ti_rs_function_2.jpg
create mode 100644 doc/Eqs/fix_ti_rs_function_2.tex
create mode 100644 doc/Eqs/fix_ti_rs_function_3.jpg
create mode 100644 doc/Eqs/fix_ti_rs_function_3.tex
create mode 100644 doc/Eqs/fix_ti_spring_force.jpg
create mode 100644 doc/Eqs/fix_ti_spring_force.tex
create mode 100644 doc/Eqs/fix_ti_spring_function_1.jpg
create mode 100644 doc/Eqs/fix_ti_spring_function_1.tex
create mode 100644 doc/Eqs/fix_ti_spring_function_2.jpg
create mode 100644 doc/Eqs/fix_ti_spring_function_2.tex
create mode 100644 doc/Eqs/fix_wall_lj1043.jpg
create mode 100644 doc/Eqs/fix_wall_lj1043.tex
create mode 100644 doc/Eqs/improper_cossq.jpg
create mode 100644 doc/Eqs/improper_cossq.tex
create mode 100644 doc/Eqs/improper_fourier.jpg
create mode 100644 doc/Eqs/improper_fourier.tex
create mode 100644 doc/Eqs/improper_ring.jpg
create mode 100644 doc/Eqs/improper_ring.tex
create mode 100644 doc/Eqs/pair_bop.jpg
create mode 100644 doc/Eqs/pair_bop.tex
create mode 100644 doc/Eqs/pair_coul_dsf.jpg
create mode 100644 doc/Eqs/pair_coul_dsf.tex
create mode 100644 doc/Eqs/pair_meam_sw_spline.jpg
create mode 100644 doc/Eqs/pair_meam_sw_spline.tex
create mode 100644 doc/Eqs/pair_mie.jpg
create mode 100644 doc/Eqs/pair_mie.tex
create mode 100644 doc/Eqs/pair_mie2.jpg
create mode 100644 doc/Eqs/pair_mie2.tex
create mode 100644 doc/Eqs/pair_nb3b_harmonic.jpg
create mode 100644 doc/Eqs/pair_nb3b_harmonic.tex
create mode 100644 doc/Eqs/pair_nm.jpg
create mode 100644 doc/Eqs/pair_nm.tex
create mode 100644 doc/Eqs/pair_tersoff.jpg
create mode 100644 doc/Eqs/pair_tersoff_mod.jpg
create mode 100644 doc/Eqs/pair_tersoff_mod.tex
create mode 100644 doc/Eqs/pair_zbl.jpg
create mode 100644 doc/Eqs/pair_zbl.tex
create mode 100755 doc/JPG/rhodo_staggered.jpg
create mode 100644 doc/PDF/PDLammps_VES.pdf
create mode 100644 doc/PDF/colvars-refman-lammps.pdf
create mode 100755 doc/PDF/kspace.pdf
create mode 100644 doc/Section_gran_models.html
create mode 100644 doc/Section_gran_models.txt
create mode 100644 doc/USER/atc/man_add_molecule.html
create mode 100644 doc/USER/atc/man_add_species.html
create mode 100644 doc/USER/atc/man_atom_weight.html
create mode 100644 doc/USER/atc/man_atomic_charge.html
create mode 100644 doc/USER/atc/man_boundary.html
create mode 100644 doc/USER/atc/man_boundary_dynamics.html
create mode 100644 doc/USER/atc/man_boundary_faceset.html
create mode 100644 doc/USER/atc/man_consistent_fe_initialization.html
create mode 100644 doc/USER/atc/man_control.html
create mode 100644 doc/USER/atc/man_control_momentum.html
create mode 100644 doc/USER/atc/man_control_thermal.html
create mode 100644 doc/USER/atc/man_control_thermal_correction_max_iterations.html
create mode 100644 doc/USER/atc/man_decomposition.html
delete mode 100644 doc/USER/atc/man_disp_control.html
create mode 100644 doc/USER/atc/man_fe_md_boundary.html
create mode 100644 doc/USER/atc/man_filter_type.html
delete mode 100644 doc/USER/atc/man_hardy_set.html
create mode 100644 doc/USER/atc/man_internal_atom_integrate.html
create mode 100644 doc/USER/atc/man_internal_element_set.html
create mode 100644 doc/USER/atc/man_kernel_function.html
create mode 100644 doc/USER/atc/man_localized_lambda.html
create mode 100644 doc/USER/atc/man_lumped_lambda_solve.html
create mode 100644 doc/USER/atc/man_mask_direction.html
create mode 100644 doc/USER/atc/man_mass_matrix.html
create mode 100644 doc/USER/atc/man_material.html
create mode 100644 doc/USER/atc/man_mesh_add_to_nodeset.html
create mode 100644 doc/USER/atc/man_mesh_create.html
create mode 100644 doc/USER/atc/man_mesh_create_elementset.html
create mode 100644 doc/USER/atc/man_mesh_create_faceset_box.html
create mode 100644 doc/USER/atc/man_mesh_create_faceset_plane.html
create mode 100644 doc/USER/atc/man_mesh_create_nodeset.html
delete mode 100644 doc/USER/atc/man_mesh_elemset.html
delete mode 100644 doc/USER/atc/man_mesh_faceset.html
delete mode 100644 doc/USER/atc/man_mesh_nodeset.html
create mode 100644 doc/USER/atc/man_mesh_nodeset_to_elementset.html
create mode 100644 doc/USER/atc/man_mesh_quadrature.html
create mode 100644 doc/USER/atc/man_mesh_read.html
create mode 100644 doc/USER/atc/man_mesh_write.html
create mode 100644 doc/USER/atc/man_momentum_time_integration.html
delete mode 100644 doc/USER/atc/man_neighbor_reset_frequency.html
create mode 100644 doc/USER/atc/man_output.html
create mode 100644 doc/USER/atc/man_output_elementset.html
create mode 100644 doc/USER/atc/man_output_nodeset.html
create mode 100644 doc/USER/atc/man_pair_interactions.html
create mode 100644 doc/USER/atc/man_poisson_solver.html
create mode 100644 doc/USER/atc/man_remove_molecule.html
create mode 100644 doc/USER/atc/man_remove_species.html
create mode 100644 doc/USER/atc/man_reset_atomic_reference_positions.html
create mode 100644 doc/USER/atc/man_reset_time.html
create mode 100644 doc/USER/atc/man_sample_frequency.html
create mode 100644 doc/USER/atc/man_set.html
create mode 100644 doc/USER/atc/man_source_integration.html
create mode 100644 doc/USER/atc/man_temperature_definition.html
delete mode 100644 doc/USER/atc/man_thermal_control.html
create mode 100644 doc/USER/atc/man_thermal_time_integration.html
delete mode 100644 doc/USER/atc/man_time_integration.html
create mode 100644 doc/USER/atc/man_track_displacement.html
delete mode 100644 doc/USER/atc/man_transfer_atomic_output.html
delete mode 100644 doc/USER/atc/man_transfer_boundary.html
delete mode 100644 doc/USER/atc/man_transfer_internal.html
delete mode 100644 doc/USER/atc/man_transfer_output.html
create mode 100644 doc/USER/atc/man_write_atom_weights.html
create mode 100644 doc/angle_fourier.html
create mode 100644 doc/angle_fourier.txt
create mode 100644 doc/angle_fourier_simple.html
create mode 100644 doc/angle_fourier_simple.txt
create mode 100644 doc/angle_quartic.html
create mode 100644 doc/angle_quartic.txt
create mode 100644 doc/body.html
create mode 100644 doc/body.txt
create mode 100644 doc/box.html
create mode 100644 doc/box.txt
create mode 100644 doc/compute_basal_atom.html
create mode 100644 doc/compute_basal_atom.txt
create mode 100644 doc/compute_body_local.html
create mode 100644 doc/compute_body_local.txt
create mode 100644 doc/compute_erotate_sphere_atom.html
create mode 100644 doc/compute_erotate_sphere_atom.txt
create mode 100644 doc/compute_inertia_molecule.html
create mode 100644 doc/compute_inertia_molecule.txt
create mode 100644 doc/compute_msd_nongauss.html
create mode 100644 doc/compute_msd_nongauss.txt
create mode 100644 doc/compute_voronoi_atom.html
create mode 100644 doc/compute_voronoi_atom.txt
create mode 100644 doc/dihedral_fourier.html
create mode 100644 doc/dihedral_fourier.txt
create mode 100644 doc/dihedral_nharmonic.html
create mode 100644 doc/dihedral_nharmonic.txt
create mode 100644 doc/dihedral_quadratic.html
create mode 100644 doc/dihedral_quadratic.txt
create mode 100644 doc/dump_molfile.html
create mode 100644 doc/dump_molfile.txt
create mode 100644 doc/fix_colvars.html
create mode 100644 doc/fix_colvars.txt
create mode 100644 doc/fix_gld.html
create mode 100644 doc/fix_gld.txt
create mode 100644 doc/fix_lb_fluid.html
create mode 100755 doc/fix_lb_fluid.txt
create mode 100644 doc/fix_lb_momentum.html
create mode 100755 doc/fix_lb_momentum.txt
create mode 100644 doc/fix_lb_pc.html
create mode 100755 doc/fix_lb_pc.txt
create mode 100644 doc/fix_lb_rigid_pc_sphere.html
create mode 100755 doc/fix_lb_rigid_pc_sphere.txt
create mode 100644 doc/fix_lb_viscous.html
create mode 100755 doc/fix_lb_viscous.txt
create mode 100644 doc/fix_nve_body.html
create mode 100755 doc/fix_nve_body.txt
create mode 100644 doc/fix_phonon.html
create mode 100644 doc/fix_phonon.txt
create mode 100644 doc/fix_reaxc_species.html
create mode 100644 doc/fix_reaxc_species.txt
create mode 100644 doc/fix_ti_rs.html
create mode 100755 doc/fix_ti_rs.txt
create mode 100644 doc/fix_ti_spring.html
create mode 100755 doc/fix_ti_spring.txt
create mode 100644 doc/fix_tune_kspace.html
create mode 100644 doc/fix_tune_kspace.txt
create mode 100644 doc/gran_cohesion_sjkr.html
create mode 100644 doc/gran_cohesion_sjkr.txt
create mode 100644 doc/gran_cohesion_sjkr2.html
create mode 100644 doc/gran_cohesion_sjkr2.txt
create mode 100644 doc/gran_model_hertz.html
create mode 100644 doc/gran_model_hertz.txt
create mode 100644 doc/gran_model_hertz_stiffness.html
create mode 100644 doc/gran_model_hertz_stiffness.txt
create mode 100644 doc/gran_model_hooke.html
create mode 100644 doc/gran_model_hooke.txt
create mode 100644 doc/gran_model_hooke_stiffness.html
create mode 100644 doc/gran_model_hooke_stiffness.txt
create mode 100644 doc/gran_rolling_friction_cdt.html
create mode 100644 doc/gran_rolling_friction_cdt.txt
create mode 100644 doc/gran_rolling_friction_epsd.html
create mode 100644 doc/gran_rolling_friction_epsd.txt
create mode 100644 doc/gran_rolling_friction_epsd2.html
create mode 100644 doc/gran_rolling_friction_epsd2.txt
create mode 100644 doc/gran_tangential_history.html
create mode 100644 doc/gran_tangential_history.txt
create mode 100644 doc/gran_tangential_no_history.html
create mode 100644 doc/gran_tangential_no_history.txt
create mode 100644 doc/group2ndx.html
create mode 100644 doc/group2ndx.txt
create mode 100644 doc/improper_cossq.html
create mode 100644 doc/improper_cossq.txt
create mode 100644 doc/improper_fourier.html
create mode 100644 doc/improper_fourier.txt
create mode 100644 doc/improper_ring.html
create mode 100644 doc/improper_ring.txt
create mode 100644 doc/liggghts_3.X_tutorial.html
create mode 100644 doc/liggghts_3.X_tutorial.txt
delete mode 100644 doc/orient.html
delete mode 100644 doc/orient.txt
delete mode 100644 doc/origin.html
delete mode 100644 doc/origin.txt
create mode 100644 doc/pair_body.html
create mode 100644 doc/pair_body.txt
create mode 100644 doc/pair_bop.html
create mode 100644 doc/pair_bop.txt
delete mode 100644 doc/pair_buck_coul.html
delete mode 100644 doc/pair_buck_coul.txt
create mode 100644 doc/pair_buck_long.html
create mode 100644 doc/pair_buck_long.txt
create mode 100644 doc/pair_lcbop.html
create mode 100644 doc/pair_lcbop.txt
create mode 100644 doc/pair_list.html
create mode 100644 doc/pair_list.txt
delete mode 100644 doc/pair_lj_coul.html
delete mode 100644 doc/pair_lj_coul.txt
create mode 100644 doc/pair_lj_long.html
create mode 100644 doc/pair_lj_long.txt
create mode 100644 doc/pair_meam_sw_spline.html
create mode 100644 doc/pair_meam_sw_spline.txt
create mode 100644 doc/pair_mie.html
create mode 100644 doc/pair_mie.txt
create mode 100644 doc/pair_nb3b_harmonic.html
create mode 100644 doc/pair_nb3b_harmonic.txt
create mode 100644 doc/pair_nm.html
create mode 100644 doc/pair_nm.txt
create mode 100644 doc/pair_tersoff_mod.html
create mode 100644 doc/pair_tersoff_mod.txt
create mode 100644 doc/pair_zbl.html
create mode 100644 doc/pair_zbl.txt
create mode 100644 doc/read_dump.html
create mode 100644 doc/read_dump.txt
create mode 100644 doc/rerun.html
create mode 100644 doc/rerun.txt
create mode 100644 doc/write_data.html
create mode 100644 doc/write_data.txt
create mode 100644 doc/write_dump.html
create mode 100644 doc/write_dump.txt
create mode 100755 examples/LAMMPS/ASPHERE/README
create mode 100755 examples/LAMMPS/ASPHERE/box/box.py
create mode 100755 examples/LAMMPS/ASPHERE/box/data.box
create mode 100755 examples/LAMMPS/ASPHERE/box/in.box
create mode 100755 examples/LAMMPS/ASPHERE/box/in.box.mp
create mode 100755 examples/LAMMPS/ASPHERE/box/log.box.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/box/log.box.mp.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/dimer/data.dimer
create mode 100755 examples/LAMMPS/ASPHERE/dimer/dimer.py
create mode 100755 examples/LAMMPS/ASPHERE/dimer/in.dimer
create mode 100755 examples/LAMMPS/ASPHERE/dimer/in.dimer.mp
create mode 100755 examples/LAMMPS/ASPHERE/dimer/log.dimer.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/dimer/log.dimer.mp.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/ellipsoid/in.ellipsoid
create mode 100755 examples/LAMMPS/ASPHERE/ellipsoid/in.ellipsoid.mp
create mode 100755 examples/LAMMPS/ASPHERE/ellipsoid/log.ellipsoid.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/ellipsoid/log.ellipsoid.mp.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/line/data.line
create mode 100755 examples/LAMMPS/ASPHERE/line/data.line.srd
create mode 100755 examples/LAMMPS/ASPHERE/line/in.line
create mode 100755 examples/LAMMPS/ASPHERE/line/in.line.srd
create mode 100755 examples/LAMMPS/ASPHERE/line/line.py
create mode 100755 examples/LAMMPS/ASPHERE/line/line.srd.py
create mode 100755 examples/LAMMPS/ASPHERE/line/line.srd.viz.py
create mode 100755 examples/LAMMPS/ASPHERE/line/line.viz.py
create mode 100755 examples/LAMMPS/ASPHERE/line/log.line.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/line/log.line.srd.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/poly/in.poly
create mode 100755 examples/LAMMPS/ASPHERE/poly/in.poly.mp
create mode 100755 examples/LAMMPS/ASPHERE/poly/log.poly.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/poly/log.poly.mp.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/star/data.star
create mode 100755 examples/LAMMPS/ASPHERE/star/in.star
create mode 100755 examples/LAMMPS/ASPHERE/star/in.star.mp
create mode 100755 examples/LAMMPS/ASPHERE/star/log.star.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/star/log.star.mp.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/star/star.py
create mode 100755 examples/LAMMPS/ASPHERE/tri/data.tri.srd
create mode 100755 examples/LAMMPS/ASPHERE/tri/in.tri.srd
create mode 100755 examples/LAMMPS/ASPHERE/tri/log.tri.srd.10Sep13
create mode 100755 examples/LAMMPS/ASPHERE/tri/tri.srd.py
create mode 100755 examples/LAMMPS/ASPHERE/tri/tri.srd.viz.py
create mode 100755 examples/LAMMPS/COUPLE/README
create mode 100755 examples/LAMMPS/COUPLE/fortran/README
create mode 100755 examples/LAMMPS/COUPLE/fortran/libfwrapper.c
create mode 100755 examples/LAMMPS/COUPLE/fortran2/LAMMPS-wrapper.cpp
create mode 100755 examples/LAMMPS/COUPLE/fortran2/LAMMPS-wrapper.h
create mode 100755 examples/LAMMPS/COUPLE/fortran2/LAMMPS.F90
create mode 100755 examples/LAMMPS/COUPLE/fortran2/README
create mode 100755 examples/LAMMPS/COUPLE/fortran2/in.simple
create mode 100755 examples/LAMMPS/COUPLE/fortran2/makefile
create mode 100755 examples/LAMMPS/COUPLE/fortran2/simple.f90
create mode 100755 examples/LAMMPS/COUPLE/lammps_quest/Makefile.g++
create mode 100755 examples/LAMMPS/COUPLE/lammps_quest/README
create mode 100755 examples/LAMMPS/COUPLE/lammps_quest/in.lammps
rename {couple => examples/LAMMPS/COUPLE}/lammps_quest/lmppath.h (100%)
create mode 100755 examples/LAMMPS/COUPLE/lammps_quest/lmpqst.cpp
rename {couple => examples/LAMMPS/COUPLE}/lammps_quest/log.lammps.1 (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_quest/log.lammps.4 (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_quest/qstexe.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_quest/si_111.in (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/Makefile.g++ (100%)
create mode 100755 examples/LAMMPS/COUPLE/lammps_spparks/README
create mode 100755 examples/LAMMPS/COUPLE/lammps_spparks/in.lammps
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/in.spparks (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/lmppath.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/lmpspk.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/log.lammps.1 (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/log.lammps.4 (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/log.spparks.1 (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/log.spparks.4 (100%)
rename {couple => examples/LAMMPS/COUPLE}/lammps_spparks/spkpath.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/Makefile.g++ (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/README (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/error.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/error.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/files.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/files.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/irregular.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/irregular.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/lammps_data_write.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/lammps_data_write.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/many2many.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/many2many.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/many2one.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/many2one.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/memory.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/memory.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/one2many.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/one2many.h (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/send2one.cpp (100%)
rename {couple => examples/LAMMPS/COUPLE}/library/send2one.h (100%)
create mode 100755 examples/LAMMPS/COUPLE/simple/README
create mode 100755 examples/LAMMPS/COUPLE/simple/in.lj
rename {couple => examples/LAMMPS/COUPLE}/simple/log.simple.c++.1 (100%)
rename {couple => examples/LAMMPS/COUPLE}/simple/log.simple.c++.4 (100%)
create mode 100755 examples/LAMMPS/COUPLE/simple/simple.c
create mode 100755 examples/LAMMPS/COUPLE/simple/simple.cpp
create mode 100755 examples/LAMMPS/COUPLE/simple/simple.f90
create mode 100755 examples/LAMMPS/ELASTIC/displace_restart.mod
create mode 100755 examples/LAMMPS/ELASTIC/displace_reverse.mod
create mode 100755 examples/LAMMPS/KAPPA/README
create mode 100755 examples/LAMMPS/KAPPA/in.heat
create mode 100755 examples/LAMMPS/KAPPA/in.heatflux
create mode 100755 examples/LAMMPS/KAPPA/in.langevin
create mode 100755 examples/LAMMPS/KAPPA/in.mp
create mode 100755 examples/LAMMPS/KAPPA/log.heat.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/log.heatflux.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/log.langevin.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/log.mp.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/profile.heat.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/profile.heatflux.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/profile.langevin.12Sep13
create mode 100755 examples/LAMMPS/KAPPA/profile.mp.12Sep13
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/Ar_thermal.mat
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/bar1d.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/bar1d_flux.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/in.bar1d
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/in.bar1d_flux
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/in.bar1d_frac_step
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_thermal/temp.init
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/Ar_ttm.mat
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/Cu_ttm.mat
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/bar1d_ttm.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/gaussianIC_ttm.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/in.bar1d_ttm
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/in.gaussianIC_ttm
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/in.no_atoms
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/in.uniform_exchange
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/in.uniform_heating
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/no_atoms.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/temp.init
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/uniform_exchange.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/uniform_exchange_init.data
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/uniform_heating.log
delete mode 100755 examples/LAMMPS/USER/atc/bar1d_two_temperature/uniform_heating_init.data
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Ar_CauchyBorn.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Ar_CauchyBorn_linear.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Au_CauchyBorn.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Au_CauchyBorn_linear.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Au_eam.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Au_eam_linear.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/Cu_CauchyBorn.mat
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_biaxial.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_shear.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_unistrain.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_unistrain_eam.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_unistrain_eam_linear.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_unistrain_linear.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/cb_volumetric.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/flying_cube.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/ftcb_constV.screen
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_biaxial
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_shear
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_unistrain
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_unistrain_eam
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_unistrain_eam_linear
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_unistrain_linear
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.cb_volumetric
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.flying_cube
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.ftcb_constV
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/in.read_xref
create mode 100755 examples/LAMMPS/USER/atc/cauchy_born/read_xref.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/Ar_ddm.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/CNT_ddm.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/Cu_cddm.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/SiGe_ddm_schrodinger.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/SiVacuum_cddm_schrodinger.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/SiVacuum_ddm_schrodinger.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/Si_ddm.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/Si_ddm_eq.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/Si_ddm_schrodinger.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/Si_ddm_thermopower.mat
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/convective_pulse.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/ddm_schrodinger.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/finite_well.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.convective_pulse
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.ddm_schrodinger
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.finite_well
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.no_atoms_ddm
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.null_material_ddm
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.poisson1d_noatoms
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.poisson2d_noatoms
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.schrodinger-poisson2d_Jconstraint
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.schrodinger-poisson2d_convective
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/in.schrodinger-poisson2d_noatoms
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/no_atoms_ddm.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/null_material_ddm.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/poisson1d_noatoms.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/poisson2d_noatoms.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/schrodinger-poisson2d_Jconstraint.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/schrodinger-poisson2d_convective.screen
create mode 100755 examples/LAMMPS/USER/atc/drift_diffusion/schrodinger-poisson2d_noatoms.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/Ar_CauchyBorn.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/Ar_CauchyBornLinear.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/Ar_damped.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/Ar_elastic.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/Ar_thermo_elastic.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/Au_elastic.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/CNT.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/CNT_electrostatic.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/CNT_electrostatic2.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/CNT_id.mat
create mode 100755 examples/LAMMPS/USER/atc/elastic/bar1d.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/bar1d_damped.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/bar1d_flux.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/bar1d_frac_step.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/bar1d_ghost_flux.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/bar1d_thermo_elastic.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/cnt_electrostatic.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/cnt_electrostatic2.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/cnt_fixed_charge.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/eam_energy.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/electron_density.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/electrostatic_bending.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/electrostatic_bending_dos.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.bar1d
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.bar1d_damped
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.bar1d_flux
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.bar1d_frac_step
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.bar1d_ghost_flux
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.bar1d_thermo_elastic
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.cnt_electrostatic
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.cnt_electrostatic2
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.cnt_fixed_charge
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.eam_energy
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.electron_density
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.electrostatic_bending
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.electrostatic_bending_dos
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.no_atoms
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.no_atoms_cb
create mode 100755 examples/LAMMPS/USER/atc/elastic/in.no_atoms_cb_linear
create mode 100755 examples/LAMMPS/USER/atc/elastic/no_atoms.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/no_atoms_cb.screen
create mode 100755 examples/LAMMPS/USER/atc/elastic/no_atoms_cb_linear.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_elastic.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_electrostatic.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_liquid.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_species.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_species_dl.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_thermal.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_visc_no_atoms.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/Ar_viscosity.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/bar1d_fluids.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/concentration.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/conducting_interface.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/dielectric.mat
create mode 100755 examples/LAMMPS/USER/atc/fluids/dielectric_interface.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/double_layer.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.bar1d_fluids
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.concentration
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.conducting_interface
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.dielectric_interface
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.double_layer
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.liquid_electrostatic
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.opp_force
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.poisson
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.shear_flow
create mode 100755 examples/LAMMPS/USER/atc/fluids/in.shear_no_atoms
create mode 100755 examples/LAMMPS/USER/atc/fluids/liquid_electrostatic.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/opp_force.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/poisson.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/shear_flow.screen
create mode 100755 examples/LAMMPS/USER/atc/fluids/shear_no_atoms.screen
create mode 100755 examples/LAMMPS/USER/atc/hardy/eshelby_static.screen
create mode 100755 examples/LAMMPS/USER/atc/hardy/in.eshelby_static
create mode 100755 examples/LAMMPS/USER/atc/hardy/nvt.data
create mode 100755 examples/LAMMPS/USER/atc/hardy/nvt.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/Ar_ttm.mat
create mode 100755 examples/LAMMPS/USER/atc/mesh/Si.mat
create mode 100755 examples/LAMMPS/USER/atc/mesh/gaussianIC1d_hex.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/gaussianIC2d_hex.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/gaussianIC2d_hex20_uniform.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/gaussianIC2d_hex27_uniform.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/gaussianIC2d_hex_uniform.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/gaussianIC2d_tet.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.gaussianIC1d_hex
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_hex
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_hex20_uniform
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_hex27_uniform
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.gaussianIC2d_tet
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.kernel2d_hex
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.kernel2d_tet
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.mesh2d_tet
create mode 100755 examples/LAMMPS/USER/atc/mesh/in.semicircle
create mode 100755 examples/LAMMPS/USER/atc/mesh/kernel2d_hex.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/kernel2d_tet.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/mesh2d_tet.screen
create mode 100755 examples/LAMMPS/USER/atc/mesh/semicircle.screen
create mode 100755 examples/LAMMPS/USER/atc/molecule/harmonic_bonds.screen
create mode 100755 examples/LAMMPS/USER/atc/molecule/in.harmonic_bonds
create mode 100755 examples/LAMMPS/USER/atc/molecule/in.polarize
create mode 100755 examples/LAMMPS/USER/atc/molecule/in.quartic_bonds
create mode 100755 examples/LAMMPS/USER/atc/molecule/in.water
create mode 100755 examples/LAMMPS/USER/atc/molecule/polarize.screen
create mode 100755 examples/LAMMPS/USER/atc/molecule/quartic_bonds.screen
create mode 100755 examples/LAMMPS/USER/atc/molecule/water.mat
create mode 100755 examples/LAMMPS/USER/atc/molecule/water.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/Ar_thermal.mat
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_all_atoms.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_combined.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_flux.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_frac_step.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_hoover.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_interpolate.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/bar1d_lumped.screen
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_all_atoms
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_combined
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_flux
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_frac_step
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_hoover
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_interpolate
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.bar1d_lumped
create mode 100755 examples/LAMMPS/USER/atc/thermal/in.no_atoms
create mode 100755 examples/LAMMPS/USER/atc/thermal/no_atoms.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/Ar_ttm.mat
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/Cu_ttm.mat
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/bar1d_ttm.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/cutout.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/gaussianIC_ttm.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.bar1d_ttm
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.cutout
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.gaussianIC_ttm
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.no_atoms
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.restart
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.uniform_exchange
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/in.uniform_heating
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/no_atoms.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/restart.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/uniform_exchange.screen
create mode 100755 examples/LAMMPS/USER/atc/two_temperature/uniform_heating.screen
copy examples/LAMMPS/{peptide => USER/colvars}/data.peptide (100%)
create mode 100755 examples/LAMMPS/USER/colvars/in.peptide-colvars
create mode 100755 examples/LAMMPS/USER/colvars/in.peptide-colvars2
create mode 100755 examples/LAMMPS/USER/colvars/log.peptide-colvars-1
create mode 100755 examples/LAMMPS/USER/colvars/log.peptide-colvars-4
create mode 100755 examples/LAMMPS/USER/colvars/log.peptide-colvars2-1
create mode 100755 examples/LAMMPS/USER/colvars/log.peptide-colvars2-4
create mode 100755 examples/LAMMPS/USER/colvars/out.colvars.state
create mode 100755 examples/LAMMPS/USER/colvars/out.colvars.traj
create mode 100755 examples/LAMMPS/USER/colvars/out2.colvars.state
create mode 100755 examples/LAMMPS/USER/colvars/out2.colvars.traj
create mode 100755 examples/LAMMPS/USER/colvars/peptide.colvars
create mode 100755 examples/LAMMPS/USER/colvars/peptide.colvars2
create mode 100755 examples/LAMMPS/USER/colvars/peptide.psf
create mode 100755 examples/LAMMPS/USER/colvars/peptide2.colvars.state
create mode 100755 examples/LAMMPS/USER/colvars/peptide2.colvars.traj
create mode 100755 examples/LAMMPS/USER/eff/ECP/SiC/bulk/data.SiC
create mode 100755 examples/LAMMPS/USER/eff/ECP/SiC/bulk/in.SiC
create mode 100755 examples/LAMMPS/USER/lb/confined_colloid/in.confined_colloids
create mode 100755 examples/LAMMPS/USER/lb/confined_colloid/results64.out
create mode 100755 examples/LAMMPS/USER/lb/dragforce/data.one_radius16d2
create mode 100755 examples/LAMMPS/USER/lb/dragforce/defaultgamma_drag.out
create mode 100755 examples/LAMMPS/USER/lb/dragforce/in.defaultgamma_drag
create mode 100755 examples/LAMMPS/USER/lb/dragforce/in.setgamma_drag
create mode 100755 examples/LAMMPS/USER/lb/dragforce/setgamma13d0_drag.out
create mode 100755 examples/LAMMPS/USER/lb/fourspheres/data.four
create mode 100755 examples/LAMMPS/USER/lb/fourspheres/fourspheres_velocity0d0001_defaultgamma.out
create mode 100755 examples/LAMMPS/USER/lb/fourspheres/fourspheres_velocity0d0001_setgamma.out
create mode 100755 examples/LAMMPS/USER/lb/fourspheres/in.fourspheres_default_gamma
create mode 100755 examples/LAMMPS/USER/lb/fourspheres/in.fourspheres_set_gamma
create mode 100755 examples/LAMMPS/USER/lb/microrheology/data.two
create mode 100755 examples/LAMMPS/USER/lb/microrheology/in.microrheology_default_gamma
create mode 100755 examples/LAMMPS/USER/lb/microrheology/in.microrheology_set_gamma
create mode 100755 examples/LAMMPS/USER/lb/microrheology/microrheology_defaultgamma.out
create mode 100755 examples/LAMMPS/USER/lb/microrheology/microrheology_setgamma.out
create mode 100755 examples/LAMMPS/USER/lb/planewall/data.one_radius16d2
create mode 100755 examples/LAMMPS/USER/lb/planewall/in.planewall_default_gamma
create mode 100755 examples/LAMMPS/USER/lb/planewall/in.planewall_set_gamma
create mode 100755 examples/LAMMPS/USER/lb/planewall/wall_defaultgamma.out
create mode 100755 examples/LAMMPS/USER/lb/planewall/wall_setgamma.out
create mode 100755 examples/LAMMPS/USER/lb/polymer/data.polymer
create mode 100755 examples/LAMMPS/USER/lb/polymer/in.polymer
create mode 100755 examples/LAMMPS/USER/lb/polymer/out.polymer
create mode 100755 examples/LAMMPS/USER/misc/basal/almg.liu
create mode 100755 examples/LAMMPS/USER/misc/basal/in.basal
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/bcc.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/bcc_relax.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/dc.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/dc_relax.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/energy_conservation.meam.sw.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/fcc.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/fcc_relax.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/hcp_relax.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/sc.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/sc_relax.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Si/single_atom.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/alpha.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/alpha_relaxation.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/beta.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/energy_conservation.meam.sw.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/fcc.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/hexagonal.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/omega.in
create mode 100755 examples/LAMMPS/USER/misc/meam_sw_spline/Ti/single_atom.in
create mode 100755 examples/LAMMPS/USER/misc/ti/in.ti_rs
create mode 100755 examples/LAMMPS/USER/misc/ti/in.ti_spring
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/README
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/data.pos
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/disp.dat
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/in.Ana
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/in.disp
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/log.lammps.example
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/map.in
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/pdisp.eps
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/phonon.bin.2000000
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/phonon.log
create mode 100755 examples/LAMMPS/USER/phonon/1-1D-mono/plot.disp
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/README
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/data.pos
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/disp.dat
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/in.Ana
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/in.disp
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/log.lammps.example
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/map.in
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/pdisp.eps
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/pdos.dat
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/phonon.bin.2000000
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/phonon.log
create mode 100755 examples/LAMMPS/USER/phonon/2-1D-diatomic/plot.disp
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.bin.6500000
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/CuPhonon.log.example
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/README
copy bench/Cu_u3.eam => examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/cuu3.eam (100%)
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/data.pos
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp-expr.dat
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp-ld.dat
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/disp.dat
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos-expr.dat
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos-ld.dat
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/dos.dat
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.EAM3D
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.disp
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/in.dos
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/log.lammps.example
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/map.in
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/pdisp.eps
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/pdos.eps
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/plot.disp
create mode 100755 examples/LAMMPS/USER/phonon/3-3D-FCC-Cu-EAM/plot.dos
create mode 100755 examples/LAMMPS/VISCOSITY/README
create mode 100755 examples/LAMMPS/VISCOSITY/in.gk.2d
create mode 100755 examples/LAMMPS/VISCOSITY/in.mp.2d
create mode 100755 examples/LAMMPS/VISCOSITY/in.nemd.2d
create mode 100755 examples/LAMMPS/VISCOSITY/in.wall.2d
create mode 100755 examples/LAMMPS/VISCOSITY/log.gk.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/log.mp.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/log.nemd.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/log.wall.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/profile.gk.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/profile.mp.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/profile.nemd.2d.12Sep13
create mode 100755 examples/LAMMPS/VISCOSITY/profile.wall.2d.12Sep13
create mode 100755 examples/LAMMPS/body/data.body
create mode 100755 examples/LAMMPS/body/in.body
create mode 100755 examples/LAMMPS/body/log.body.18Feb13.linux.1
create mode 100755 examples/LAMMPS/body/log.body.18Feb13.linux.4
create mode 100755 examples/LAMMPS/colloid/log.colloid.18Feb13.linux.1
create mode 100755 examples/LAMMPS/colloid/log.colloid.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/colloid/log.colloid.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/colloid/log.colloid.9Jan12.linux.4
create mode 100755 examples/LAMMPS/comb/data.comb3-OHCCu
create mode 100755 examples/LAMMPS/comb/ffield.comb3
create mode 100755 examples/LAMMPS/comb/in.comb3
create mode 100755 examples/LAMMPS/comb/lib.comb3
create mode 100755 examples/LAMMPS/comb/log.comb.Cu.18Feb13.linux.1
create mode 100755 examples/LAMMPS/comb/log.comb.Cu.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/comb/log.comb.Cu.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/comb/log.comb.Cu.9Jan12.linux.4
create mode 100755 examples/LAMMPS/comb/log.comb.Cu2O.elastic.18Feb13.linux.1
create mode 100755 examples/LAMMPS/comb/log.comb.Cu2O.elastic.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/comb/log.comb.Cu2O.elastic.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/comb/log.comb.Cu2O.elastic.9Jan12.linux.4
delete mode 100755 examples/LAMMPS/comb/log.comb.CuaS.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/comb/log.comb.CuaS.9Jan12.linux.4
create mode 100755 examples/LAMMPS/comb/log.comb.HfO2.18Feb13.linux.1
create mode 100755 examples/LAMMPS/comb/log.comb.HfO2.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/comb/log.comb.HfO2.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/comb/log.comb.HfO2.9Jan12.linux.4
create mode 100755 examples/LAMMPS/comb/log.comb.Si.18Feb13.linux.1
create mode 100755 examples/LAMMPS/comb/log.comb.Si.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/comb/log.comb.Si.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/comb/log.comb.Si.9Jan12.linux.4
create mode 100755 examples/LAMMPS/comb/log.comb.Si.elastic.18Feb13.linux.1
create mode 100755 examples/LAMMPS/comb/log.comb.Si.elastic.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/comb/log.comb.Si.elastic.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/comb/log.comb.Si.elastic.9Jan12.linux.4
create mode 100755 examples/LAMMPS/comb/log.comb3.4Nov13.linux.1
create mode 100755 examples/LAMMPS/comb/log.comb3.4Nov13.linux.4
create mode 100755 examples/LAMMPS/crack/log.crack.18Feb13.linux.1
create mode 100755 examples/LAMMPS/crack/log.crack.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/crack/log.crack.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/crack/log.crack.9Jan12.linux.4
create mode 100755 examples/LAMMPS/dipole/log.dipole.18Feb13.linux.1
create mode 100755 examples/LAMMPS/dipole/log.dipole.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/dipole/log.dipole.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/dipole/log.dipole.9Jan12.linux.4
create mode 100755 examples/LAMMPS/dreiding/log.dreiding.18Feb13.linux.1
create mode 100755 examples/LAMMPS/dreiding/log.dreiding.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/dreiding/log.dreiding.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/dreiding/log.dreiding.9Jan12.linux.4
create mode 100755 examples/LAMMPS/eim/log.eim.18Feb13.linux.1
create mode 100755 examples/LAMMPS/eim/log.eim.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/eim/log.eim.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/eim/log.eim.9Jan12.linux.4
create mode 100755 examples/LAMMPS/ellipse/log.ellipse.gayberne.18Feb13.linux.1
create mode 100755 examples/LAMMPS/ellipse/log.ellipse.gayberne.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/ellipse/log.ellipse.gayberne.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/ellipse/log.ellipse.gayberne.9Jan12.linux.4
create mode 100755 examples/LAMMPS/ellipse/log.ellipse.resquared.18Feb13.linux.1
create mode 100755 examples/LAMMPS/ellipse/log.ellipse.resquared.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/ellipse/log.ellipse.resquared.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/ellipse/log.ellipse.resquared.9Jan12.linux.4
create mode 100755 examples/LAMMPS/flow/log.flow.couette.18Feb13.linux.1
create mode 100755 examples/LAMMPS/flow/log.flow.couette.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/flow/log.flow.couette.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/flow/log.flow.couette.9Jan12.linux.4
create mode 100755 examples/LAMMPS/flow/log.flow.pois.18Feb13.linux.1
create mode 100755 examples/LAMMPS/flow/log.flow.pois.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/flow/log.flow.pois.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/flow/log.flow.pois.9Jan12.linux.4
create mode 100755 examples/LAMMPS/friction/log.friction.18Feb13.linux.1
create mode 100755 examples/LAMMPS/friction/log.friction.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/friction/log.friction.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/friction/log.friction.9Jan12.linux.4
create mode 100755 examples/LAMMPS/gpu/log.gpu.melt.2.5.18Feb13.linux.1
create mode 100755 examples/LAMMPS/gpu/log.gpu.melt.2.5.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/gpu/log.gpu.melt.2.5.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/gpu/log.gpu.melt.2.5.9Jan12.linux.4
create mode 100755 examples/LAMMPS/gpu/log.gpu.melt.5.0.18Feb13.linux.1
create mode 100755 examples/LAMMPS/gpu/log.gpu.melt.5.0.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/gpu/log.gpu.melt.5.0.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/gpu/log.gpu.melt.5.0.9Jan12.linux.4
create mode 100755 examples/LAMMPS/gpu/log.gpu.phosphate.18Feb13.linux.1
create mode 100755 examples/LAMMPS/gpu/log.gpu.phosphate.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/gpu/log.gpu.phosphate.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/gpu/log.gpu.phosphate.9Jan12.linux.4
create mode 100755 examples/LAMMPS/gpu/log.gpu.rhodo.18Feb13.linux.1
create mode 100755 examples/LAMMPS/gpu/log.gpu.rhodo.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/gpu/log.gpu.rhodo.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/gpu/log.gpu.rhodo.9Jan12.linux.4
create mode 100755 examples/LAMMPS/hugoniostat/log.hugoniostat.18Feb13.linux.1
create mode 100755 examples/LAMMPS/hugoniostat/log.hugoniostat.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/hugoniostat/log.hugoniostat.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/hugoniostat/log.hugoniostat.9Jan12.linux.4
create mode 100755 examples/LAMMPS/indent/log.indent.18Feb13.linux.1
create mode 100755 examples/LAMMPS/indent/log.indent.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/indent/log.indent.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/indent/log.indent.9Jan12.linux.4
create mode 100755 examples/LAMMPS/indent/log.indent.min.18Feb13.linux.1
create mode 100755 examples/LAMMPS/indent/log.indent.min.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/indent/log.indent.min.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/indent/log.indent.min.9Jan12.linux.4
create mode 100755 examples/LAMMPS/kim/log.kim.lj.26Jul13.mac_mpi.1
create mode 100755 examples/LAMMPS/kim/log.kim.lj.26Jul13.mac_mpi.4
delete mode 100755 examples/LAMMPS/kim/log.kim.lj.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/kim/log.kim.lj.9Jan12.linux.4
create mode 100755 examples/LAMMPS/kim/log.kim.lj.lmp.26Jul13.mac_mpi.1
create mode 100755 examples/LAMMPS/kim/log.kim.lj.lmp.26Jul13.mac_mpi.4
delete mode 100755 examples/LAMMPS/kim/log.kim.lj.lmp.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/kim/log.kim.lj.lmp.9Jan12.linux.4
create mode 100755 examples/LAMMPS/meam/log.meam.18Feb13.linux.1
create mode 100755 examples/LAMMPS/meam/log.meam.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/meam/log.meam.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/meam/log.meam.9Jan12.linux.4
create mode 100755 examples/LAMMPS/meam/log.meam.shear.18Feb13.linux.1
create mode 100755 examples/LAMMPS/meam/log.meam.shear.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/meam/log.meam.shear.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/meam/log.meam.shear.9Jan12.linux.4
create mode 100755 examples/LAMMPS/melt/log.melt.18Feb13.linux.1
create mode 100755 examples/LAMMPS/melt/log.melt.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/melt/log.melt.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/melt/log.melt.9Jan12.linux.4
create mode 100755 examples/LAMMPS/micelle/log.micelle.18Feb13.linux.1
create mode 100755 examples/LAMMPS/micelle/log.micelle.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/micelle/log.micelle.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/micelle/log.micelle.9Jan12.linux.4
create mode 100755 examples/LAMMPS/min/log.min.18Feb13.linux.1
create mode 100755 examples/LAMMPS/min/log.min.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/min/log.min.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/min/log.min.9Jan12.linux.4
create mode 100755 examples/LAMMPS/min/log.min.box.18Feb13.linux.1
create mode 100755 examples/LAMMPS/min/log.min.box.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/min/log.min.box.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/min/log.min.box.9Jan12.linux.4
create mode 100755 examples/LAMMPS/msst/log.msst.18Feb13.linux.1
create mode 100755 examples/LAMMPS/msst/log.msst.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/msst/log.msst.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/msst/log.msst.9Jan12.linux.4
create mode 100755 examples/LAMMPS/neb/log.neb.hop1.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/neb/log.neb.hop1.9Jan12.linux.4
create mode 100755 examples/LAMMPS/neb/log.neb.hop2.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/neb/log.neb.hop2.9Jan12.linux.4
create mode 100755 examples/LAMMPS/nemd/log.nemd.18Feb13.linux.1
create mode 100755 examples/LAMMPS/nemd/log.nemd.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/nemd/log.nemd.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/nemd/log.nemd.9Jan12.linux.4
create mode 100755 examples/LAMMPS/obstacle/log.obstacle.18Feb13.linux.1
create mode 100755 examples/LAMMPS/obstacle/log.obstacle.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/obstacle/log.obstacle.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/obstacle/log.obstacle.9Jan12.linux.4
create mode 100755 examples/LAMMPS/peptide/log.peptide.18Feb13.linux.1
create mode 100755 examples/LAMMPS/peptide/log.peptide.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/peptide/log.peptide.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/peptide/log.peptide.9Jan12.linux.4
create mode 100755 examples/LAMMPS/peri/log.peri.18Feb13.linux.1
create mode 100755 examples/LAMMPS/peri/log.peri.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/peri/log.peri.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/peri/log.peri.9Jan12.linux.4
create mode 100755 examples/LAMMPS/prd/log.prd.0.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/prd/log.prd.0.9Jan12.linux.4
create mode 100755 examples/LAMMPS/prd/log.prd.1.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/prd/log.prd.1.9Jan12.linux.4
create mode 100755 examples/LAMMPS/prd/log.prd.18Feb13.linux.4
create mode 100755 examples/LAMMPS/prd/log.prd.2.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/prd/log.prd.2.9Jan12.linux.4
create mode 100755 examples/LAMMPS/prd/log.prd.3.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/prd/log.prd.3.9Jan12.linux.4
delete mode 100755 examples/LAMMPS/prd/log.prd.9Jan12.linux.4
create mode 100755 examples/LAMMPS/reax/Fluorographene/README
create mode 100755 examples/LAMMPS/reax/Fluorographene/data.FC
create mode 100755 examples/LAMMPS/reax/Fluorographene/dumpnpt.xyz
create mode 100755 examples/LAMMPS/reax/Fluorographene/ffield.reax.FC
create mode 100755 examples/LAMMPS/reax/Fluorographene/in.FC
create mode 100755 examples/LAMMPS/reax/Fluorographene/log.FC
create mode 100755 examples/LAMMPS/reax/log.reax.rdx.18Feb13.linux.1
create mode 100755 examples/LAMMPS/reax/log.reax.rdx.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/reax/log.reax.rdx.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/reax/log.reax.rdx.9Jan12.linux.4
create mode 100755 examples/LAMMPS/reax/log.reax.tatb.18Feb13.linux.1
create mode 100755 examples/LAMMPS/reax/log.reax.tatb.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/reax/log.reax.tatb.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/reax/log.reax.tatb.9Jan12.linux.4
create mode 100755 examples/LAMMPS/reax/log.reaxc.rdx.18Feb13.linux.1
create mode 100755 examples/LAMMPS/reax/log.reaxc.rdx.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/reax/log.reaxc.rdx.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/reax/log.reaxc.rdx.9Jan12.linux.4
create mode 100755 examples/LAMMPS/reax/log.reaxc.tatb.18Feb13.linux.1
create mode 100755 examples/LAMMPS/reax/log.reaxc.tatb.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/reax/log.reaxc.tatb.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/reax/log.reaxc.tatb.9Jan12.linux.4
create mode 100755 examples/LAMMPS/rigid/data.rigid.tnr
create mode 100755 examples/LAMMPS/rigid/in.rigid.tnr
create mode 100755 examples/LAMMPS/rigid/log.rigid.18Feb13.linux.1
create mode 100755 examples/LAMMPS/rigid/log.rigid.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/rigid/log.rigid.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/rigid/log.rigid.9Jan12.linux.4
create mode 100755 examples/LAMMPS/rigid/log.rigid.poems.18Feb13.linux.1
create mode 100755 examples/LAMMPS/rigid/log.rigid.poems.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/rigid/log.rigid.poems.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/rigid/log.rigid.poems.9Jan12.linux.4
create mode 100755 examples/LAMMPS/rigid/log.rigid.poems2.18Feb13.linux.1
create mode 100755 examples/LAMMPS/rigid/log.rigid.poems2.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/rigid/log.rigid.poems2.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/rigid/log.rigid.poems2.9Jan12.linux.4
create mode 100755 examples/LAMMPS/shear/log.shear.18Feb13.linux.1
create mode 100755 examples/LAMMPS/shear/log.shear.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/shear/log.shear.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/shear/log.shear.9Jan12.linux.4
create mode 100755 examples/LAMMPS/shear/log.shear.void.18Feb13.linux.1
create mode 100755 examples/LAMMPS/shear/log.shear.void.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/shear/log.shear.void.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/shear/log.shear.void.9Jan12.linux.4
create mode 100755 examples/LAMMPS/srd/log.srd.mixture.18Feb13.linux.1
create mode 100755 examples/LAMMPS/srd/log.srd.mixture.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/srd/log.srd.mixture.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/srd/log.srd.mixture.9Jan12.linux.4
create mode 100755 examples/LAMMPS/srd/log.srd.pure.18Feb13.linux.1
create mode 100755 examples/LAMMPS/srd/log.srd.pure.18Feb13.linux.4
delete mode 100755 examples/LAMMPS/srd/log.srd.pure.9Jan12.linux.1
delete mode 100755 examples/LAMMPS/srd/log.srd.pure.9Jan12.linux.4
create mode 100755 examples/LAMMPS/tad/log.tad.0.18Feb13.linux.3
delete mode 100755 examples/LAMMPS/tad/log.tad.0.9Jan12.linux.3
create mode 100755 examples/LAMMPS/tad/log.tad.1.18Feb13.linux.3
delete mode 100755 examples/LAMMPS/tad/log.tad.1.9Jan12.linux.3
create mode 100755 examples/LAMMPS/tad/log.tad.18Feb13.linux.3
create mode 100755 examples/LAMMPS/tad/log.tad.2.18Feb13.linux.3
delete mode 100755 examples/LAMMPS/tad/log.tad.2.9Jan12.linux.3
delete mode 100755 examples/LAMMPS/tad/log.tad.9Jan12.linux.3
create mode 100755 examples/LAMMPS/tad/log.tad.neb.18Feb13.linux.3
delete mode 100755 examples/LAMMPS/tad/log.tad.neb.9Jan12.linux.3
create mode 100755 examples/LAMMPS/voronoi/in.voronoi
create mode 100755 examples/LAMMPS/voronoi/log.voronoi.4Aug13.macos.1
create mode 100755 examples/LAMMPS/voronoi/log.voronoi.4Aug13.macos.4
rename examples/LIGGGHTS/Tutorials_public/chute_wear/{ => meshes}/insertion_face.stl (100%)
rename examples/LIGGGHTS/Tutorials_public/chute_wear/{ => meshes}/simple_chute.stl (100%)
rename examples/LIGGGHTS/Tutorials_public/{mesh_tet/post/dummy => chute_wear/post/.gitignore} (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/chute_wear/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/chute_wear/run.config
rename examples/LIGGGHTS/Tutorials_public/{packing/post/dummy => cohesion/post/.gitignore} (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/cohesion/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/cohesion/run.config
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/contactModels/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/contactModels/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/contactModels/run.config
rename examples/LIGGGHTS/Tutorials_public/conveyor/{ => meshes}/box.stl (100%)
rename examples/LIGGGHTS/Tutorials_public/conveyor/{ => meshes}/conveyor.stl (100%)
rename examples/LIGGGHTS/Tutorials_public/conveyor/{ => meshes}/insertion_face.stl (100%)
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/conveyor/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/conveyor/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/conveyor/run.config
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/heatTransfer_1/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/heatTransfer_1/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/heatTransfer_1/run.config
delete mode 100644 examples/LIGGGHTS/Tutorials_public/heatTransfer_2/LOG
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/heatTransfer_2/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/heatTransfer_2/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/heatTransfer_2/run.config
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/hysteresis/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/hysteresis/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/hysteresis/run.config
create mode 100644 examples/LIGGGHTS/Tutorials_public/insert_stream/in.insert_stream_reset_timestep
rename examples/LIGGGHTS/Tutorials_public/insert_stream/{ => meshes}/face.stl (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/insert_stream/post.py
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/insert_stream/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/insert_stream/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/insert_stream/run.config
delete mode 100644 examples/LIGGGHTS/Tutorials_public/insert_stream/state.pvsm
rename examples/LIGGGHTS/Tutorials_public/meshGran/{ => meshes}/insertion_face.stl (100%)
rename examples/LIGGGHTS/Tutorials_public/meshGran/{ => meshes}/mesh.stl (100%)
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/meshGran/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/meshGran/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/meshGran/run.config
rename examples/LIGGGHTS/Tutorials_public/mesh_tet/{ => data}/test.vtk (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/mesh_tet/log.liggghts
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/mesh_tet/post/.gitignore (100%)
create mode 100644 examples/LIGGGHTS/Tutorials_public/mesh_tet/run.config
rename examples/LIGGGHTS/Tutorials_public/movingMeshGran/{ => meshes}/bucket.stl (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/movingMeshGran/post.py
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/movingMeshGran/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/movingMeshGran/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/movingMeshGran/run.config
delete mode 100644 examples/LIGGGHTS/Tutorials_public/packing/log.liggghts
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/packing/post/.gitignore (100%)
create mode 100644 examples/LIGGGHTS/Tutorials_public/packing/run.config
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/sph_1/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/sph_1/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/sph_1/run.config
copy doc/fix_wall_region_sph.html => examples/LIGGGHTS/Tutorials_public/sph_2/post/.gitignore (100%)
delete mode 100644 examples/LIGGGHTS/Tutorials_public/sph_2/post/dummy
create mode 100644 examples/LIGGGHTS/Tutorials_public/sph_2/run.config
create mode 100755 lib/atc/ATC_Coupling.cpp
create mode 100755 lib/atc/ATC_Coupling.h
create mode 100755 lib/atc/ATC_CouplingEnergy.cpp
create mode 100755 lib/atc/ATC_CouplingEnergy.h
create mode 100755 lib/atc/ATC_CouplingMass.cpp
create mode 100755 lib/atc/ATC_CouplingMass.h
create mode 100755 lib/atc/ATC_CouplingMomentum.cpp
create mode 100755 lib/atc/ATC_CouplingMomentum.h
create mode 100755 lib/atc/ATC_CouplingMomentumEnergy.cpp
create mode 100755 lib/atc/ATC_CouplingMomentumEnergy.h
delete mode 100755 lib/atc/ATC_HardyKernel.cpp
delete mode 100755 lib/atc/ATC_HardyKernel.h
create mode 100755 lib/atc/ATC_Method.cpp
create mode 100755 lib/atc/ATC_Method.h
delete mode 100755 lib/atc/ATC_TransferHardy.cpp
delete mode 100755 lib/atc/ATC_TransferHardy.h
create mode 100755 lib/atc/ATC_TransferKernel.cpp
create mode 100755 lib/atc/ATC_TransferKernel.h
create mode 100755 lib/atc/ATC_TransferPartitionOfUnity.cpp
create mode 100755 lib/atc/ATC_TransferPartitionOfUnity.h
delete mode 100755 lib/atc/ATC_TransferThermal.cpp
delete mode 100755 lib/atc/ATC_TransferThermal.h
delete mode 100755 lib/atc/ATC_TransferUtility.cpp
create mode 100755 lib/atc/AtomToMoleculeTransfer.cpp
create mode 100755 lib/atc/AtomToMoleculeTransfer.h
create mode 100755 lib/atc/BodyForce.cpp
create mode 100755 lib/atc/BodyForce.h
create mode 100755 lib/atc/CBLattice.cpp
create mode 100755 lib/atc/CBLattice.h
create mode 100755 lib/atc/CauchyBorn.cpp
create mode 100755 lib/atc/CauchyBorn.h
create mode 100755 lib/atc/CbEam.h
create mode 100755 lib/atc/CbLjCut.h
create mode 100755 lib/atc/CbLjSmoothLinear.h
create mode 100755 lib/atc/CbPotential.cpp
create mode 100755 lib/atc/CbPotential.h
create mode 100755 lib/atc/ChargeRegulator.cpp
create mode 100755 lib/atc/ChargeRegulator.h
create mode 100755 lib/atc/ConcentrationRegulator.cpp
create mode 100755 lib/atc/ConcentrationRegulator.h
create mode 100755 lib/atc/DependencyManager.h
create mode 100755 lib/atc/DislocationExtractor.h
create mode 100755 lib/atc/ElectronChargeDensity.cpp
create mode 100755 lib/atc/ElectronChargeDensity.h
create mode 100755 lib/atc/ElectronDragPower.cpp
create mode 100755 lib/atc/ElectronDragPower.h
create mode 100755 lib/atc/ExtrinsicModelDriftDiffusion.cpp
create mode 100755 lib/atc/ExtrinsicModelDriftDiffusion.h
create mode 100755 lib/atc/ExtrinsicModelElectrostatic.cpp
create mode 100755 lib/atc/ExtrinsicModelElectrostatic.h
create mode 100755 lib/atc/FE_Interpolate.cpp
create mode 100755 lib/atc/FE_Interpolate.h
create mode 100755 lib/atc/FE_Quadrature.h
create mode 100755 lib/atc/FieldManager.cpp
create mode 100755 lib/atc/FieldManager.h
create mode 100755 lib/atc/Function.cpp
create mode 100755 lib/atc/Function.h
create mode 100755 lib/atc/FundamentalAtomicQuantity.cpp
create mode 100755 lib/atc/FundamentalAtomicQuantity.h
create mode 100755 lib/atc/GhostManager.cpp
create mode 100755 lib/atc/GhostManager.h
create mode 100755 lib/atc/InterscaleOperators.cpp
create mode 100755 lib/atc/InterscaleOperators.h
create mode 100755 lib/atc/KD_Tree.cpp
create mode 100755 lib/atc/KD_Tree.h
create mode 100755 lib/atc/KernelFunction.cpp
create mode 100755 lib/atc/KernelFunction.h
create mode 100755 lib/atc/KinetoThermostat.cpp
create mode 100755 lib/atc/KinetoThermostat.h
create mode 100755 lib/atc/LinearSolver.cpp
create mode 100755 lib/atc/LinearSolver.h
create mode 100755 lib/atc/MPI_Wrappers.cpp
create mode 100755 lib/atc/MPI_Wrappers.h
create mode 100755 lib/atc/Makefile.lammps.empty
copy lib/atc/{Makefile.lammps => Makefile.lammps.installed} (100%)
create mode 100755 lib/atc/Makefile.lammps.linalg
create mode 100755 lib/atc/Makefile.mingw32-cross
create mode 100755 lib/atc/Makefile.mingw32-cross-mpi
create mode 100755 lib/atc/Makefile.mingw64-cross
create mode 100755 lib/atc/Makefile.mingw64-cross-mpi
create mode 100755 lib/atc/Makefile.mpic++
create mode 100755 lib/atc/MeshReader.cpp
create mode 100755 lib/atc/MeshReader.h
create mode 100755 lib/atc/MoleculeSet.cpp
create mode 100755 lib/atc/MoleculeSet.h
create mode 100755 lib/atc/NonLinearSolver.cpp
create mode 100755 lib/atc/NonLinearSolver.h
create mode 100755 lib/atc/PaqAtcUtility.cpp
create mode 100755 lib/atc/PaqAtcUtility.h
create mode 100755 lib/atc/ParDenseMatrix.h
create mode 100755 lib/atc/ParDiagonalMatrix.cpp
create mode 100755 lib/atc/ParDiagonalMatrix.h
create mode 100755 lib/atc/ParSparseMatrix.cpp
create mode 100755 lib/atc/ParSparseMatrix.h
create mode 100755 lib/atc/PerAtomQuantity-inl.h
create mode 100755 lib/atc/PerAtomQuantity.h
create mode 100755 lib/atc/PerAtomQuantityLibrary.cpp
create mode 100755 lib/atc/PerAtomQuantityLibrary.h
create mode 100755 lib/atc/PerPairQuantity.cpp
create mode 100755 lib/atc/PerPairQuantity.h
create mode 100755 lib/atc/PhysicsModel.cpp
delete mode 100755 lib/atc/PhysicsModelThermal.cpp
delete mode 100755 lib/atc/PhysicsModelThermal.h
delete mode 100755 lib/atc/PhysicsModelTwoTemperature.cpp
delete mode 100755 lib/atc/PhysicsModelTwoTemperature.h
create mode 100755 lib/atc/PoissonSolver.cpp
create mode 100755 lib/atc/PoissonSolver.h
create mode 100755 lib/atc/PolynomialSolver.cpp
create mode 100755 lib/atc/PolynomialSolver.h
create mode 100755 lib/atc/Quadrature.cpp
create mode 100755 lib/atc/SchrodingerSolver.cpp
create mode 100755 lib/atc/SchrodingerSolver.h
create mode 100755 lib/atc/ShapeFunction.h
delete mode 100755 lib/atc/Solver.cpp
delete mode 100755 lib/atc/Solver.h
create mode 100755 lib/atc/SpeciesTimeIntegrator.cpp
create mode 100755 lib/atc/SpeciesTimeIntegrator.h
create mode 100755 lib/atc/Stress.cpp
create mode 100755 lib/atc/Stress.h
delete mode 100755 lib/atc/StringManip.h
create mode 100755 lib/atc/ThermalTimeIntegrator.cpp
create mode 100755 lib/atc/ThermalTimeIntegrator.h
create mode 100755 lib/atc/TransferLibrary.cpp
create mode 100755 lib/atc/TransferLibrary.h
create mode 100755 lib/atc/TransferOperator.cpp
create mode 100755 lib/atc/TransferOperator.h
create mode 100755 lib/atc/ViscousStress.cpp
create mode 100755 lib/atc/ViscousStress.h
create mode 100755 lib/atc/VoigtOperations.h
create mode 100755 lib/atc/WeakEquation.h
create mode 100755 lib/atc/WeakEquationChargeDiffusion.cpp
create mode 100755 lib/atc/WeakEquationChargeDiffusion.h
create mode 100755 lib/atc/WeakEquationDiffusion.cpp
create mode 100755 lib/atc/WeakEquationDiffusion.h
create mode 100755 lib/atc/WeakEquationElectronContinuity.cpp
create mode 100755 lib/atc/WeakEquationElectronContinuity.h
create mode 100755 lib/atc/WeakEquationElectronMomentum.cpp
create mode 100755 lib/atc/WeakEquationElectronMomentum.h
create mode 100755 lib/atc/WeakEquationElectronTemperature.cpp
create mode 100755 lib/atc/WeakEquationElectronTemperature.h
create mode 100755 lib/atc/WeakEquationMassDiffusion.cpp
create mode 100755 lib/atc/WeakEquationMassDiffusion.h
create mode 100755 lib/atc/WeakEquationMomentum.cpp
create mode 100755 lib/atc/WeakEquationMomentum.h
create mode 100755 lib/atc/WeakEquationPhononTemperature.cpp
create mode 100755 lib/atc/WeakEquationPhononTemperature.h
create mode 100755 lib/atc/WeakEquationPoisson.cpp
create mode 100755 lib/atc/WeakEquationPoisson.h
create mode 100755 lib/atc/WeakEquationSchrodinger.cpp
create mode 100755 lib/atc/WeakEquationSchrodinger.h
delete mode 100755 lib/atc/XT_Function.cpp
delete mode 100755 lib/atc/XT_Function.h
create mode 100755 lib/awpmd/Makefile.lammps.empty
rename lib/awpmd/{Makefile.lammps => Makefile.lammps.installed} (100%)
create mode 100755 lib/awpmd/Makefile.lammps.linalg
create mode 100755 lib/awpmd/Makefile.mingw32-cross
create mode 100755 lib/awpmd/Makefile.mingw32-cross-mpi
create mode 100755 lib/awpmd/Makefile.mingw64-cross
create mode 100755 lib/awpmd/Makefile.mingw64-cross-mpi
copy lib/colvars/{Makefile.lammps => Makefile.lammps.debug} (100%)
rename lib/colvars/{Makefile.lammps => Makefile.lammps.empty} (100%)
create mode 100755 lib/colvars/Makefile.mingw32-cross
create mode 100755 lib/colvars/Makefile.mingw32-cross-mpi
create mode 100755 lib/colvars/Makefile.mingw64-cross
create mode 100755 lib/colvars/Makefile.mingw64-cross-mpi
delete mode 100755 lib/cuda/binning.cu
delete mode 100755 lib/cuda/binning_cu.h
delete mode 100755 lib/cuda/binning_kernel.cu
create mode 100755 lib/gpu/Makefile.lammps.mac_ocl
create mode 100755 lib/gpu/Makefile.lammps.mingw-cross
create mode 100755 lib/gpu/Makefile.lammps.opencl
rename lib/gpu/{Makefile.lammps => Makefile.lammps.standard} (100%)
create mode 100755 lib/gpu/Makefile.linux.double
create mode 100755 lib/gpu/Makefile.linux.mixed
create mode 100755 lib/gpu/Makefile.mingw32-cross
create mode 100755 lib/gpu/Makefile.mingw32-cross-mpi
create mode 100755 lib/gpu/Makefile.mingw64-cross
create mode 100755 lib/gpu/Makefile.mingw64-cross-mpi
create mode 100755 lib/gpu/Makefile.xk7
delete mode 100755 lib/gpu/geryon/nvc_device.h
delete mode 100755 lib/gpu/geryon/nvc_macros.h
delete mode 100755 lib/gpu/geryon/nvc_texture.h
create mode 100755 lib/gpu/geryon/ucl_matrix.h
create mode 100755 lib/gpu/geryon/ucl_s_obj_help.h
create mode 100755 lib/gpu/geryon/ucl_vector.h
create mode 100755 lib/gpu/lal_base_dipole.cpp
create mode 100755 lib/gpu/lal_base_dipole.h
create mode 100755 lib/gpu/lal_base_three.cpp
create mode 100755 lib/gpu/lal_base_three.h
create mode 100755 lib/gpu/lal_beck.cpp
create mode 100755 lib/gpu/lal_beck.cu
create mode 100755 lib/gpu/lal_beck.h
create mode 100755 lib/gpu/lal_beck_ext.cpp
create mode 100755 lib/gpu/lal_born.cpp
create mode 100755 lib/gpu/lal_born.cu
create mode 100755 lib/gpu/lal_born.h
create mode 100755 lib/gpu/lal_born_coul_long.cpp
create mode 100755 lib/gpu/lal_born_coul_long.cu
create mode 100755 lib/gpu/lal_born_coul_long.h
create mode 100755 lib/gpu/lal_born_coul_long_ext.cpp
create mode 100755 lib/gpu/lal_born_coul_wolf.cpp
create mode 100755 lib/gpu/lal_born_coul_wolf.cu
create mode 100755 lib/gpu/lal_born_coul_wolf.h
create mode 100755 lib/gpu/lal_born_coul_wolf_ext.cpp
create mode 100755 lib/gpu/lal_born_ext.cpp
create mode 100755 lib/gpu/lal_colloid.cpp
create mode 100755 lib/gpu/lal_colloid.cu
create mode 100755 lib/gpu/lal_colloid.h
create mode 100755 lib/gpu/lal_colloid_ext.cpp
create mode 100755 lib/gpu/lal_coul_dsf.cpp
create mode 100755 lib/gpu/lal_coul_dsf.cu
create mode 100755 lib/gpu/lal_coul_dsf.h
create mode 100755 lib/gpu/lal_coul_dsf_ext.cpp
create mode 100755 lib/gpu/lal_dipole_lj.cpp
create mode 100755 lib/gpu/lal_dipole_lj.cu
create mode 100755 lib/gpu/lal_dipole_lj.h
create mode 100755 lib/gpu/lal_dipole_lj_ext.cpp
create mode 100755 lib/gpu/lal_dipole_lj_sf.cpp
create mode 100755 lib/gpu/lal_dipole_lj_sf.cu
create mode 100755 lib/gpu/lal_dipole_lj_sf.h
create mode 100755 lib/gpu/lal_dipole_lj_sf_ext.cpp
create mode 100755 lib/gpu/lal_gauss.cpp
create mode 100755 lib/gpu/lal_gauss.cu
create mode 100755 lib/gpu/lal_gauss.h
create mode 100755 lib/gpu/lal_gauss_ext.cpp
create mode 100755 lib/gpu/lal_lj_coul_debye.cpp
create mode 100755 lib/gpu/lal_lj_coul_debye.cu
create mode 100755 lib/gpu/lal_lj_coul_debye.h
create mode 100755 lib/gpu/lal_lj_coul_debye_ext.cpp
create mode 100755 lib/gpu/lal_lj_coul_msm.cpp
create mode 100755 lib/gpu/lal_lj_coul_msm.cu
create mode 100755 lib/gpu/lal_lj_coul_msm.h
create mode 100755 lib/gpu/lal_lj_coul_msm_ext.cpp
create mode 100755 lib/gpu/lal_lj_dsf.cpp
create mode 100755 lib/gpu/lal_lj_dsf.cu
create mode 100755 lib/gpu/lal_lj_dsf.h
create mode 100755 lib/gpu/lal_lj_dsf_ext.cpp
create mode 100755 lib/gpu/lal_mie.cpp
create mode 100755 lib/gpu/lal_mie.cu
create mode 100755 lib/gpu/lal_mie.h
create mode 100755 lib/gpu/lal_mie_ext.cpp
create mode 100755 lib/gpu/lal_soft.cpp
create mode 100755 lib/gpu/lal_soft.cu
create mode 100755 lib/gpu/lal_soft.h
create mode 100755 lib/gpu/lal_soft_ext.cpp
create mode 100755 lib/gpu/lal_sw.cpp
create mode 100755 lib/gpu/lal_sw.cu
create mode 100755 lib/gpu/lal_sw.h
create mode 100755 lib/gpu/lal_sw_ext.cpp
create mode 100755 lib/gpu/lal_yukawa_colloid.cpp
create mode 100755 lib/gpu/lal_yukawa_colloid.cu
create mode 100755 lib/gpu/lal_yukawa_colloid.h
create mode 100755 lib/gpu/lal_yukawa_colloid_ext.cpp
create mode 100755 lib/linalg/Makefile.mingw32-cross
create mode 100755 lib/linalg/Makefile.mingw32-cross-mpi
create mode 100755 lib/linalg/Makefile.mingw64-cross
create mode 100755 lib/linalg/Makefile.mingw64-cross-mpi
delete mode 100755 lib/linalg/Makefile.mingw_cross
create mode 100755 lib/linalg/disnan.f
create mode 100755 lib/linalg/dlaisnan.f
create mode 100755 lib/linalg/zdotc.f
create mode 100755 lib/linalg/zdscal.f
create mode 100755 lib/linalg/zhpr.f
create mode 100755 lib/linalg/zpptrf.f
create mode 100755 lib/linalg/zpptri.f
create mode 100755 lib/linalg/zscal.f
create mode 100755 lib/linalg/ztpmv.f
create mode 100755 lib/linalg/ztpsv.f
create mode 100755 lib/linalg/ztptri.f
delete mode 100755 lib/meam/Makefile.lammps
create mode 100755 lib/meam/Makefile.mingw32-cross
create mode 100755 lib/meam/Makefile.mingw32-cross-mpi
create mode 100755 lib/meam/Makefile.mingw64-cross
create mode 100755 lib/meam/Makefile.mingw64-cross-mpi
rename lib/poems/{Makefile.lammps => Makefile.lammps.empty} (100%)
create mode 100755 lib/poems/Makefile.mingw32-cross
create mode 100755 lib/poems/Makefile.mingw32-cross-mpi
create mode 100755 lib/poems/Makefile.mingw64-cross
create mode 100755 lib/poems/Makefile.mingw64-cross-mpi
delete mode 100755 lib/poems/Makefile.storm
delete mode 100755 lib/reax/Makefile.g77
delete mode 100755 lib/reax/Makefile.lammps
create mode 100755 potentials/BNC.tersoff
create mode 100755 potentials/MOH.nb3b.harmonic
create mode 100755 potentials/Si.b.meam.sw.spline
create mode 100755 potentials/Si.tersoff.mod
create mode 100755 potentials/Ti.meam.sw.spline
create mode 100755 potentials/ffield.comb3
delete mode 100755 potentials/ffield.reax.Al_Al0_AlN
create mode 100755 potentials/ffield.reax.FC
create mode 100755 potentials/lib.comb3
create mode 100755 python/install.py
delete mode 100755 python/setup.py
delete mode 100755 python/setup_serial.py
create mode 100755 regress/benchmark.py
create mode 100755 regress/melt/in.melt
create mode 100755 regress/melt/log.melt.linux.4
create mode 100755 regress/min/in.min
create mode 100755 regress/min/in.min.box
create mode 100755 regress/min/log.min.box.linux.4
create mode 100755 regress/min/log.min.linux.4
create mode 100755 regress/regression.sh
delete mode 100644 src/ASPHERE/Install.sh
create mode 100644 src/BODY/body_nparticle.cpp
create mode 100644 src/BODY/body_nparticle.h
create mode 100644 src/BODY/compute_body_local.cpp
create mode 100644 src/BODY/compute_body_local.h
create mode 100644 src/BODY/fix_nve_body.cpp
create mode 100644 src/BODY/fix_nve_body.h
create mode 100644 src/BODY/pair_body.cpp
create mode 100644 src/BODY/pair_body.h
delete mode 100644 src/CLASS2/Install.sh
delete mode 100644 src/COLLOID/Install.sh
delete mode 100644 src/DIPOLE/Install.sh
delete mode 100644 src/DIPOLE/pair_dipole_cut.cpp
delete mode 100644 src/DIPOLE/pair_dipole_cut.h
create mode 100755 src/DIPOLE/pair_lj_cut_dipole_cut.cpp
create mode 100755 src/DIPOLE/pair_lj_cut_dipole_cut.h
create mode 100755 src/DIPOLE/pair_lj_cut_dipole_long.cpp
create mode 100755 src/DIPOLE/pair_lj_cut_dipole_long.h
create mode 100755 src/DIPOLE/pair_lj_long_dipole_long.cpp
create mode 100755 src/DIPOLE/pair_lj_long_dipole_long.h
delete mode 100644 src/FLD/Install.sh
delete mode 100644 src/GPU/Package.sh
create mode 100644 src/GPU/pair_beck_gpu.cpp
create mode 100644 src/GPU/pair_beck_gpu.h
create mode 100644 src/GPU/pair_born_coul_long_gpu.cpp
create mode 100644 src/GPU/pair_born_coul_long_gpu.h
create mode 100644 src/GPU/pair_born_coul_wolf_gpu.cpp
create mode 100644 src/GPU/pair_born_coul_wolf_gpu.h
create mode 100644 src/GPU/pair_born_gpu.cpp
create mode 100644 src/GPU/pair_born_gpu.h
create mode 100644 src/GPU/pair_colloid_gpu.cpp
create mode 100644 src/GPU/pair_colloid_gpu.h
create mode 100644 src/GPU/pair_coul_dsf_gpu.cpp
create mode 100644 src/GPU/pair_coul_dsf_gpu.h
create mode 100644 src/GPU/pair_gauss_gpu.cpp
create mode 100644 src/GPU/pair_gauss_gpu.h
create mode 100644 src/GPU/pair_lj_cut_coul_debye_gpu.cpp
create mode 100644 src/GPU/pair_lj_cut_coul_debye_gpu.h
create mode 100644 src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
create mode 100644 src/GPU/pair_lj_cut_coul_dsf_gpu.h
create mode 100644 src/GPU/pair_lj_cut_coul_msm_gpu.cpp
create mode 100644 src/GPU/pair_lj_cut_coul_msm_gpu.h
create mode 100755 src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
create mode 100755 src/GPU/pair_lj_cut_dipole_cut_gpu.h
create mode 100755 src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
create mode 100755 src/GPU/pair_lj_sf_dipole_sf_gpu.h
create mode 100644 src/GPU/pair_mie_cut_gpu.cpp
create mode 100644 src/GPU/pair_mie_cut_gpu.h
create mode 100644 src/GPU/pair_soft_gpu.cpp
create mode 100644 src/GPU/pair_soft_gpu.h
create mode 100644 src/GPU/pair_sw_gpu.cpp
create mode 100644 src/GPU/pair_sw_gpu.h
create mode 100644 src/GPU/pair_yukawa_colloid_gpu.cpp
create mode 100644 src/GPU/pair_yukawa_colloid_gpu.h
create mode 100644 src/Install.sh
create mode 100644 src/KIM/Makefile.lammps
delete mode 100644 src/KSPACE/Install.sh
create mode 100644 src/KSPACE/commgrid.cpp
create mode 100644 src/KSPACE/commgrid.h
create mode 100644 src/KSPACE/ewald_disp.cpp
create mode 100644 src/KSPACE/ewald_disp.h
create mode 100644 src/KSPACE/fix_tune_kspace.cpp
create mode 100644 src/KSPACE/fix_tune_kspace.h
create mode 100644 src/KSPACE/msm.cpp
create mode 100644 src/KSPACE/msm.h
create mode 100644 src/KSPACE/msm_cg.cpp
create mode 100644 src/KSPACE/msm_cg.h
create mode 100644 src/KSPACE/pair_born_coul_msm.cpp
create mode 100644 src/KSPACE/pair_born_coul_msm.h
create mode 100644 src/KSPACE/pair_buck_coul_msm.cpp
create mode 100644 src/KSPACE/pair_buck_coul_msm.h
create mode 100644 src/KSPACE/pair_buck_long_coul_long.cpp
create mode 100644 src/KSPACE/pair_buck_long_coul_long.h
create mode 100644 src/KSPACE/pair_coul_msm.cpp
create mode 100644 src/KSPACE/pair_coul_msm.h
create mode 100644 src/KSPACE/pair_lj_charmm_coul_msm.cpp
create mode 100644 src/KSPACE/pair_lj_charmm_coul_msm.h
delete mode 100644 src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
delete mode 100644 src/KSPACE/pair_lj_cut_coul_long_tip4p.h
create mode 100644 src/KSPACE/pair_lj_cut_coul_msm.cpp
create mode 100644 src/KSPACE/pair_lj_cut_coul_msm.h
create mode 100644 src/KSPACE/pair_lj_cut_tip4p_long.cpp
create mode 100644 src/KSPACE/pair_lj_cut_tip4p_long.h
create mode 100644 src/KSPACE/pair_lj_long_coul_long.cpp
create mode 100644 src/KSPACE/pair_lj_long_coul_long.h
create mode 100755 src/KSPACE/pair_lj_long_tip4p_long.cpp
create mode 100755 src/KSPACE/pair_lj_long_tip4p_long.h
create mode 100644 src/KSPACE/pair_tip4p_long.cpp
create mode 100644 src/KSPACE/pair_tip4p_long.h
create mode 100755 src/KSPACE/pppm_disp.cpp
create mode 100755 src/KSPACE/pppm_disp.h
create mode 100755 src/KSPACE/pppm_disp_tip4p.cpp
create mode 100755 src/KSPACE/pppm_disp_tip4p.h
create mode 100644 src/KSPACE/pppm_old.cpp
create mode 100644 src/KSPACE/pppm_old.h
create mode 100755 src/KSPACE/pppm_stagger.cpp
create mode 100755 src/KSPACE/pppm_stagger.h
create mode 100644 src/MAKE/Makefile.chama
create mode 100644 src/MAKE/Makefile.fedora_debug
delete mode 100755 src/MAKE/Makefile.serial_icc
delete mode 100644 src/MANYBODY/Install.sh
create mode 100644 src/MANYBODY/pair_bop.cpp
create mode 100644 src/MANYBODY/pair_bop.h
create mode 100644 src/MANYBODY/pair_comb3.cpp
create mode 100644 src/MANYBODY/pair_comb3.h
create mode 100644 src/MANYBODY/pair_lcbop.cpp
create mode 100644 src/MANYBODY/pair_lcbop.h
create mode 100644 src/MANYBODY/pair_nb3b_harmonic.cpp
create mode 100644 src/MANYBODY/pair_nb3b_harmonic.h
create mode 100644 src/MANYBODY/pair_tersoff_mod.cpp
create mode 100644 src/MANYBODY/pair_tersoff_mod.h
delete mode 100644 src/MC/Install.sh
create mode 100644 src/MISC/compute_msd_nongauss.cpp
create mode 100644 src/MISC/compute_msd_nongauss.h
create mode 100644 src/MISC/compute_ti.cpp
create mode 100644 src/MISC/compute_ti.h
create mode 100644 src/MISC/fix_efield.cpp
create mode 100644 src/MISC/fix_efield.h
create mode 100644 src/MISC/fix_evaporate.cpp
rename src/{ => MISC}/fix_evaporate.h (100%)
create mode 100644 src/MISC/fix_gld.cpp
create mode 100644 src/MISC/fix_gld.h
create mode 100644 src/MISC/fix_orient_fcc.cpp
rename src/{ => MISC}/fix_orient_fcc.h (100%)
create mode 100644 src/MISC/fix_thermal_conductivity.cpp
rename src/{ => MISC}/fix_thermal_conductivity.h (100%)
create mode 100644 src/MISC/fix_ttm.cpp
rename src/{ => MISC}/fix_ttm.h (100%)
create mode 100644 src/MISC/fix_viscosity.cpp
rename src/{ => MISC}/fix_viscosity.h (100%)
create mode 100644 src/MISC/pair_nm_cut.cpp
create mode 100644 src/MISC/pair_nm_cut.h
create mode 100644 src/MISC/pair_nm_cut_coul_cut.cpp
create mode 100644 src/MISC/pair_nm_cut_coul_cut.h
create mode 100644 src/MISC/pair_nm_cut_coul_long.cpp
create mode 100644 src/MISC/pair_nm_cut_coul_long.h
delete mode 100644 src/MOLECULE/Install.sh
delete mode 100644 src/MOLECULE/angle_hybrid.cpp
delete mode 100644 src/MOLECULE/angle_hybrid.h
delete mode 100644 src/MOLECULE/dihedral_hybrid.cpp
delete mode 100644 src/MOLECULE/dihedral_hybrid.h
delete mode 100644 src/MOLECULE/improper_hybrid.cpp
delete mode 100644 src/MOLECULE/improper_hybrid.h
create mode 100644 src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
create mode 100644 src/MOLECULE/pair_lj_cut_tip4p_cut.h
create mode 100644 src/MOLECULE/pair_tip4p_cut.cpp
create mode 100644 src/MOLECULE/pair_tip4p_cut.h
create mode 100644 src/Makefile.shlib
delete mode 100644 src/OPT/Package.sh
delete mode 100644 src/OPT/pair_lj_cut_coul_long_tip4p_opt.cpp
delete mode 100644 src/OPT/pair_lj_cut_coul_long_tip4p_opt.h
create mode 100644 src/OPT/pair_lj_cut_tip4p_long_opt.cpp
create mode 100644 src/OPT/pair_lj_cut_tip4p_long_opt.h
create mode 100644 src/OPT/pair_lj_long_coul_long_opt.cpp
create mode 100644 src/OPT/pair_lj_long_coul_long_opt.h
delete mode 100644 src/PERI/Install.sh
create mode 100644 src/PERI/pair_peri_ves.cpp
create mode 100644 src/PERI/pair_peri_ves.h
create mode 100644 src/Purge.list
delete mode 100644 src/REPLICA/Install.sh
create mode 100644 src/RIGID/compute_erotate_rigid.cpp
create mode 100644 src/RIGID/compute_erotate_rigid.h
create mode 100644 src/RIGID/compute_ke_rigid.cpp
create mode 100644 src/RIGID/compute_ke_rigid.h
create mode 100644 src/RIGID/fix_rigid.cpp
create mode 100644 src/RIGID/fix_rigid.h
create mode 100644 src/RIGID/fix_rigid_nh.cpp
create mode 100644 src/RIGID/fix_rigid_nh.h
create mode 100644 src/RIGID/fix_rigid_nph.cpp
create mode 100644 src/RIGID/fix_rigid_nph.h
create mode 100644 src/RIGID/fix_rigid_npt.cpp
create mode 100644 src/RIGID/fix_rigid_npt.h
create mode 100644 src/RIGID/fix_rigid_nve.cpp
create mode 100644 src/RIGID/fix_rigid_nve.h
create mode 100644 src/RIGID/fix_rigid_nvt.cpp
create mode 100644 src/RIGID/fix_rigid_nvt.h
create mode 100644 src/RIGID/fix_rigid_small.cpp
create mode 100644 src/RIGID/fix_rigid_small.h
delete mode 100644 src/SHOCK/Install.sh
delete mode 100644 src/SRD/Install.sh
create mode 100644 src/STUBS/Makefile.mingw32-cross
create mode 100644 src/STUBS/Makefile.mingw64-cross
delete mode 100644 src/USER-CG-CMM/Package.sh
delete mode 100644 src/USER-CG-CMM/angle_cg_cmm.cpp
delete mode 100644 src/USER-CG-CMM/angle_cg_cmm.h
delete mode 100644 src/USER-CG-CMM/cg_cmm_parms.cpp
delete mode 100644 src/USER-CG-CMM/cg_cmm_parms.h
delete mode 100644 src/USER-CG-CMM/pair_cg_cmm.cpp
delete mode 100644 src/USER-CG-CMM/pair_cg_cmm.h
delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_cut.cpp
delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_cut.h
delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
delete mode 100644 src/USER-CG-CMM/pair_cg_cmm_coul_long.h
create mode 100644 src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp
create mode 100644 src/USER-CG-CMM/pair_lj_sdk_coul_msm.h
create mode 100755 src/USER-COLVARS/Install.sh
create mode 100644 src/USER-COLVARS/README
create mode 100644 src/USER-COLVARS/colvarproxy_lammps.cpp
create mode 100644 src/USER-COLVARS/colvarproxy_lammps.h
create mode 100644 src/USER-COLVARS/fix_colvars.cpp
create mode 100644 src/USER-COLVARS/fix_colvars.h
create mode 100644 src/USER-COLVARS/group_ndx.cpp
create mode 100644 src/USER-COLVARS/group_ndx.h
delete mode 100644 src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.cpp
delete mode 100644 src/USER-CUDA/pair_cg_cmm_coul_cut_cuda.h
delete mode 100644 src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.cpp
delete mode 100644 src/USER-CUDA/pair_cg_cmm_coul_debye_cuda.h
delete mode 100644 src/USER-CUDA/pair_cg_cmm_coul_long_cuda.cpp
delete mode 100644 src/USER-CUDA/pair_cg_cmm_coul_long_cuda.h
delete mode 100644 src/USER-CUDA/pair_cg_cmm_cuda.cpp
delete mode 100644 src/USER-CUDA/pair_cg_cmm_cuda.h
delete mode 100644 src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.cpp
delete mode 100644 src/USER-CUDA/pair_lj_sdk_coul_cut_cuda.h
delete mode 100644 src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.cpp
delete mode 100644 src/USER-CUDA/pair_lj_sdk_coul_debye_cuda.h
delete mode 100644 src/USER-EFF/Install.sh
delete mode 100644 src/USER-EWALDN/Install.sh
delete mode 100644 src/USER-EWALDN/README
delete mode 100644 src/USER-EWALDN/ewald_n.cpp
delete mode 100644 src/USER-EWALDN/ewald_n.h
delete mode 100644 src/USER-EWALDN/math_complex.h
delete mode 100644 src/USER-EWALDN/math_vector.h
delete mode 100644 src/USER-EWALDN/pair_buck_coul.cpp
delete mode 100644 src/USER-EWALDN/pair_buck_coul.h
delete mode 100644 src/USER-EWALDN/pair_lj_coul.cpp
delete mode 100644 src/USER-EWALDN/pair_lj_coul.h
create mode 100755 src/USER-LB/README
create mode 100755 src/USER-LB/fix_lb_fluid.cpp
create mode 100755 src/USER-LB/fix_lb_fluid.h
create mode 100755 src/USER-LB/fix_lb_momentum.cpp
create mode 100755 src/USER-LB/fix_lb_momentum.h
create mode 100755 src/USER-LB/fix_lb_pc.cpp
create mode 100755 src/USER-LB/fix_lb_pc.h
create mode 100755 src/USER-LB/fix_lb_rigid_pc_sphere.cpp
create mode 100755 src/USER-LB/fix_lb_rigid_pc_sphere.h
create mode 100755 src/USER-LB/fix_lb_viscous.cpp
create mode 100755 src/USER-LB/fix_lb_viscous.h
create mode 100644 src/USER-MISC/angle_fourier.cpp
create mode 100644 src/USER-MISC/angle_fourier.h
create mode 100644 src/USER-MISC/angle_fourier_simple.cpp
create mode 100644 src/USER-MISC/angle_fourier_simple.h
create mode 100644 src/USER-MISC/angle_quartic.cpp
create mode 100644 src/USER-MISC/angle_quartic.h
create mode 100644 src/USER-MISC/compute_basal_atom.cpp
create mode 100644 src/USER-MISC/compute_basal_atom.h
create mode 100644 src/USER-MISC/dihedral_fourier.cpp
create mode 100644 src/USER-MISC/dihedral_fourier.h
create mode 100644 src/USER-MISC/dihedral_nharmonic.cpp
create mode 100644 src/USER-MISC/dihedral_nharmonic.h
create mode 100644 src/USER-MISC/dihedral_quadratic.cpp
create mode 100644 src/USER-MISC/dihedral_quadratic.h
create mode 100755 src/USER-MISC/fix_ti_rs.cpp
create mode 100755 src/USER-MISC/fix_ti_rs.h
create mode 100755 src/USER-MISC/fix_ti_spring.cpp
create mode 100755 src/USER-MISC/fix_ti_spring.h
create mode 100644 src/USER-MISC/improper_cossq.cpp
create mode 100644 src/USER-MISC/improper_cossq.h
create mode 100644 src/USER-MISC/improper_fourier.cpp
create mode 100644 src/USER-MISC/improper_fourier.h
create mode 100644 src/USER-MISC/improper_ring.cpp
create mode 100644 src/USER-MISC/improper_ring.h
delete mode 100644 src/USER-MISC/pair_dipole_sf.cpp
delete mode 100644 src/USER-MISC/pair_dipole_sf.h
create mode 100644 src/USER-MISC/pair_list.cpp
create mode 100644 src/USER-MISC/pair_list.h
create mode 100755 src/USER-MISC/pair_lj_sf_dipole_sf.cpp
create mode 100755 src/USER-MISC/pair_lj_sf_dipole_sf.h
create mode 100644 src/USER-MISC/pair_meam_sw_spline.cpp
create mode 100644 src/USER-MISC/pair_meam_sw_spline.h
create mode 100644 src/USER-MOLFILE/Install.sh
create mode 100644 src/USER-MOLFILE/Makefile.lammps
create mode 100644 src/USER-MOLFILE/README
create mode 100644 src/USER-MOLFILE/dump_molfile.cpp
create mode 100644 src/USER-MOLFILE/dump_molfile.h
create mode 100644 src/USER-MOLFILE/molfile_interface.cpp
create mode 100644 src/USER-MOLFILE/molfile_interface.h
create mode 100644 src/USER-MOLFILE/molfile_plugin.h
create mode 100644 src/USER-MOLFILE/reader_molfile.cpp
create mode 100644 src/USER-MOLFILE/reader_molfile.h
create mode 100644 src/USER-MOLFILE/vmdplugin.h
delete mode 100644 src/USER-OMP/Package.sh
create mode 100644 src/USER-OMP/angle_fourier_omp.cpp
create mode 100644 src/USER-OMP/angle_fourier_omp.h
create mode 100644 src/USER-OMP/angle_fourier_simple_omp.cpp
create mode 100644 src/USER-OMP/angle_fourier_simple_omp.h
create mode 100644 src/USER-OMP/angle_quartic_omp.cpp
create mode 100644 src/USER-OMP/angle_quartic_omp.h
create mode 100644 src/USER-OMP/dihedral_fourier_omp.cpp
create mode 100644 src/USER-OMP/dihedral_fourier_omp.h
create mode 100644 src/USER-OMP/dihedral_nharmonic_omp.cpp
create mode 100644 src/USER-OMP/dihedral_nharmonic_omp.h
create mode 100644 src/USER-OMP/dihedral_quadratic_omp.cpp
create mode 100644 src/USER-OMP/dihedral_quadratic_omp.h
create mode 100644 src/USER-OMP/domain_omp.cpp
create mode 100644 src/USER-OMP/fix_nh_asphere_omp.cpp
create mode 100644 src/USER-OMP/fix_nh_asphere_omp.h
create mode 100644 src/USER-OMP/fix_nh_omp.cpp
create mode 100644 src/USER-OMP/fix_nh_omp.h
create mode 100644 src/USER-OMP/fix_nh_sphere_omp.cpp
create mode 100644 src/USER-OMP/fix_nh_sphere_omp.h
create mode 100644 src/USER-OMP/fix_nph_asphere_omp.cpp
create mode 100644 src/USER-OMP/fix_nph_asphere_omp.h
create mode 100644 src/USER-OMP/fix_nph_omp.cpp
create mode 100644 src/USER-OMP/fix_nph_omp.h
create mode 100644 src/USER-OMP/fix_nph_sphere_omp.cpp
create mode 100644 src/USER-OMP/fix_nph_sphere_omp.h
create mode 100644 src/USER-OMP/fix_nphug_omp.cpp
create mode 100644 src/USER-OMP/fix_nphug_omp.h
create mode 100644 src/USER-OMP/fix_npt_asphere_omp.cpp
create mode 100644 src/USER-OMP/fix_npt_asphere_omp.h
create mode 100644 src/USER-OMP/fix_npt_omp.cpp
create mode 100644 src/USER-OMP/fix_npt_omp.h
create mode 100644 src/USER-OMP/fix_npt_sphere_omp.cpp
create mode 100644 src/USER-OMP/fix_npt_sphere_omp.h
create mode 100644 src/USER-OMP/fix_nve_omp.cpp
create mode 100644 src/USER-OMP/fix_nve_omp.h
create mode 100644 src/USER-OMP/fix_nvt_asphere_omp.cpp
create mode 100644 src/USER-OMP/fix_nvt_asphere_omp.h
create mode 100644 src/USER-OMP/fix_nvt_omp.cpp
create mode 100644 src/USER-OMP/fix_nvt_omp.h
create mode 100644 src/USER-OMP/fix_nvt_sllod_omp.cpp
create mode 100644 src/USER-OMP/fix_nvt_sllod_omp.h
create mode 100644 src/USER-OMP/fix_nvt_sphere_omp.cpp
create mode 100644 src/USER-OMP/fix_nvt_sphere_omp.h
create mode 100644 src/USER-OMP/fix_rigid_nh_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_nh_omp.h
create mode 100644 src/USER-OMP/fix_rigid_nph_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_nph_omp.h
create mode 100644 src/USER-OMP/fix_rigid_npt_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_npt_omp.h
create mode 100644 src/USER-OMP/fix_rigid_nve_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_nve_omp.h
create mode 100644 src/USER-OMP/fix_rigid_nvt_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_nvt_omp.h
create mode 100644 src/USER-OMP/fix_rigid_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_omp.h
create mode 100644 src/USER-OMP/fix_rigid_small_omp.cpp
create mode 100644 src/USER-OMP/fix_rigid_small_omp.h
create mode 100644 src/USER-OMP/improper_cossq_omp.cpp
create mode 100644 src/USER-OMP/improper_cossq_omp.h
create mode 100644 src/USER-OMP/improper_fourier_omp.cpp
create mode 100644 src/USER-OMP/improper_fourier_omp.h
create mode 100644 src/USER-OMP/improper_ring_omp.cpp
create mode 100644 src/USER-OMP/improper_ring_omp.h
create mode 100644 src/USER-OMP/msm_cg_omp.cpp
create mode 100644 src/USER-OMP/msm_cg_omp.h
create mode 100755 src/USER-OMP/msm_omp.cpp
create mode 100755 src/USER-OMP/msm_omp.h
create mode 100755 src/USER-OMP/pair_born_coul_msm_omp.cpp
create mode 100755 src/USER-OMP/pair_born_coul_msm_omp.h
create mode 100755 src/USER-OMP/pair_buck_coul_msm_omp.cpp
create mode 100755 src/USER-OMP/pair_buck_coul_msm_omp.h
delete mode 100644 src/USER-OMP/pair_buck_coul_omp.cpp
delete mode 100644 src/USER-OMP/pair_buck_coul_omp.h
create mode 100644 src/USER-OMP/pair_buck_long_coul_long_omp.cpp
create mode 100644 src/USER-OMP/pair_buck_long_coul_long_omp.h
create mode 100644 src/USER-OMP/pair_coul_dsf_omp.cpp
create mode 100644 src/USER-OMP/pair_coul_dsf_omp.h
create mode 100755 src/USER-OMP/pair_coul_msm_omp.cpp
create mode 100755 src/USER-OMP/pair_coul_msm_omp.h
delete mode 100644 src/USER-OMP/pair_dipole_cut_omp.cpp
delete mode 100644 src/USER-OMP/pair_dipole_cut_omp.h
delete mode 100644 src/USER-OMP/pair_dipole_sf_omp.cpp
delete mode 100644 src/USER-OMP/pair_dipole_sf_omp.h
create mode 100755 src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp
create mode 100755 src/USER-OMP/pair_lj_charmm_coul_msm_omp.h
delete mode 100644 src/USER-OMP/pair_lj_charmm_coul_pppm_omp.cpp
delete mode 100644 src/USER-OMP/pair_lj_charmm_coul_pppm_omp.h
delete mode 100644 src/USER-OMP/pair_lj_class2_coul_pppm_omp.cpp
delete mode 100644 src/USER-OMP/pair_lj_class2_coul_pppm_omp.h
delete mode 100644 src/USER-OMP/pair_lj_coul_omp.cpp
delete mode 100644 src/USER-OMP/pair_lj_coul_omp.h
create mode 100644 src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_cut_coul_dsf_omp.h
delete mode 100644 src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
delete mode 100644 src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
create mode 100755 src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp
create mode 100755 src/USER-OMP/pair_lj_cut_coul_msm_omp.h
delete mode 100644 src/USER-OMP/pair_lj_cut_coul_pppm_omp.cpp
delete mode 100644 src/USER-OMP/pair_lj_cut_coul_pppm_omp.h
delete mode 100644 src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.cpp
delete mode 100644 src/USER-OMP/pair_lj_cut_coul_pppm_tip4p_omp.h
create mode 100755 src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp
create mode 100755 src/USER-OMP/pair_lj_cut_dipole_cut_omp.h
create mode 100644 src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_cut_tip4p_cut_omp.h
create mode 100644 src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_cut_tip4p_long_omp.h
create mode 100644 src/USER-OMP/pair_lj_long_coul_long_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_long_coul_long_omp.h
create mode 100644 src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_long_tip4p_long_omp.h
create mode 100644 src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp
create mode 100644 src/USER-OMP/pair_lj_sdk_coul_msm_omp.h
create mode 100755 src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp
create mode 100755 src/USER-OMP/pair_lj_sf_dipole_sf_omp.h
create mode 100644 src/USER-OMP/pair_nb3b_harmonic_omp.cpp
create mode 100644 src/USER-OMP/pair_nb3b_harmonic_omp.h
create mode 100644 src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp
create mode 100644 src/USER-OMP/pair_nm_cut_coul_cut_omp.h
create mode 100644 src/USER-OMP/pair_nm_cut_coul_long_omp.cpp
create mode 100644 src/USER-OMP/pair_nm_cut_coul_long_omp.h
create mode 100644 src/USER-OMP/pair_nm_cut_omp.cpp
create mode 100644 src/USER-OMP/pair_nm_cut_omp.h
create mode 100644 src/USER-OMP/pair_tersoff_mod_omp.cpp
create mode 100644 src/USER-OMP/pair_tersoff_mod_omp.h
create mode 100644 src/USER-OMP/pair_tip4p_cut_omp.cpp
create mode 100644 src/USER-OMP/pair_tip4p_cut_omp.h
create mode 100644 src/USER-OMP/pair_tip4p_long_omp.cpp
create mode 100644 src/USER-OMP/pair_tip4p_long_omp.h
create mode 100644 src/USER-OMP/pair_zbl_omp.cpp
create mode 100644 src/USER-OMP/pair_zbl_omp.h
create mode 100644 src/USER-OMP/pppm_disp_omp.cpp
create mode 100644 src/USER-OMP/pppm_disp_omp.h
create mode 100644 src/USER-OMP/pppm_disp_tip4p_omp.cpp
create mode 100644 src/USER-OMP/pppm_disp_tip4p_omp.h
delete mode 100644 src/USER-OMP/pppm_proxy.cpp
delete mode 100644 src/USER-OMP/pppm_proxy.h
delete mode 100644 src/USER-OMP/pppm_tip4p_proxy.cpp
delete mode 100644 src/USER-OMP/pppm_tip4p_proxy.h
create mode 100644 src/USER-OMP/respa_omp.cpp
create mode 100644 src/USER-OMP/respa_omp.h
create mode 100644 src/USER-PHONON/Install.sh
create mode 100644 src/USER-PHONON/README
create mode 100644 src/USER-PHONON/fix_phonon.cpp
create mode 100644 src/USER-PHONON/fix_phonon.h
delete mode 100755 src/USER-REAXC/Install.sh
create mode 100644 src/USER-REAXC/compute_spec_atom.cpp
create mode 100644 src/USER-REAXC/compute_spec_atom.h
create mode 100644 src/USER-REAXC/fix_reaxc_species.cpp
create mode 100644 src/USER-REAXC/fix_reaxc_species.h
delete mode 100644 src/USER-SPH/Install.sh
create mode 100755 src/VORONOI/Install.sh
create mode 100644 src/VORONOI/Makefile.lammps
create mode 100644 src/VORONOI/README
create mode 100644 src/VORONOI/compute_voronoi_atom.cpp
create mode 100644 src/VORONOI/compute_voronoi_atom.h
delete mode 100644 src/WINDOWS/LAMMPS.sln
delete mode 100644 src/WINDOWS/LAMMPS.vcproj
delete mode 100644 src/WINDOWS/LAMMPS.vsmacros
delete mode 100644 src/WINDOWS/LIGGGHTS-PUBLIC.vcxproj
delete mode 100644 src/WINDOWS/LIGGGHTS-PUBLIC_VS2012.sln
delete mode 100644 src/WINDOWS/README-PUBLIC_VS2012.txt
delete mode 100644 src/WINDOWS/README.txt
delete mode 100644 src/WINDOWS/README_VS2012.txt
delete mode 100644 src/WINDOWS/STUBS.vcproj
delete mode 100644 src/WINDOWS/STUBS.vcxproj
delete mode 100644 src/WINDOWS/extra/dirent.h
delete mode 100644 src/WINDOWS/extra/erf.h
delete mode 100644 src/WINDOWS/extra/erf_namd.c
delete mode 100644 src/WINDOWS/extra/fftw2/FFTW2dll.dll
delete mode 100644 src/WINDOWS/extra/fftw2/FFTW2dll.lib
delete mode 100644 src/WINDOWS/extra/fftw2/FFTW2st.lib
delete mode 100644 src/WINDOWS/extra/fftw2/RFFTW2dll.dll
delete mode 100644 src/WINDOWS/extra/fftw2/RFFTW2dll.lib
delete mode 100644 src/WINDOWS/extra/fftw2/RFFTW2st.lib
delete mode 100644 src/WINDOWS/extra/fftw2/fftw.h
delete mode 100644 src/WINDOWS/extra/fftw2/x64/FFTW2dll.dll
delete mode 100644 src/WINDOWS/extra/fftw2/x64/FFTW2dll.lib
delete mode 100644 src/WINDOWS/extra/fftw2/x64/FFTW2st.lib
delete mode 100644 src/WINDOWS/extra/fftw2/x64/RFFTW2dll.dll
delete mode 100644 src/WINDOWS/extra/fftw2/x64/RFFTW2dll.lib
delete mode 100644 src/WINDOWS/extra/fftw2/x64/RFFTW2st.lib
delete mode 100644 src/WINDOWS/extra/inttypes.h
delete mode 100644 src/WINDOWS/extra/sleep.cpp
delete mode 100644 src/WINDOWS/extra/sleep.h
delete mode 100644 src/WINDOWS/extra/stdint.h
delete mode 100644 src/WINDOWS/extra/sys/time.h
delete mode 100644 src/WINDOWS/extra/unistd.h
delete mode 100644 src/WINDOWS/settings/style_angle.h
delete mode 100644 src/WINDOWS/settings/style_atom.h
delete mode 100644 src/WINDOWS/settings/style_bond.h
delete mode 100644 src/WINDOWS/settings/style_command.h
delete mode 100644 src/WINDOWS/settings/style_compute.h
delete mode 100644 src/WINDOWS/settings/style_dihedral.h
delete mode 100644 src/WINDOWS/settings/style_dump.h
delete mode 100644 src/WINDOWS/settings/style_fix.h
delete mode 100644 src/WINDOWS/settings/style_improper.h
delete mode 100644 src/WINDOWS/settings/style_integrate.h
delete mode 100644 src/WINDOWS/settings/style_kspace.h
delete mode 100644 src/WINDOWS/settings/style_minimize.h
delete mode 100644 src/WINDOWS/settings/style_pair.h
delete mode 100644 src/WINDOWS/settings/style_region.h
delete mode 100644 src/XTC/Install.sh
create mode 100644 src/angle_hybrid.cpp
create mode 100644 src/angle_hybrid.h
create mode 100644 src/atom_map.cpp
create mode 100644 src/atom_masks.h
create mode 100644 src/atom_vec_body.cpp
create mode 100644 src/atom_vec_body.h
create mode 100644 src/body.cpp
create mode 100644 src/body.h
create mode 100644 src/citeme.cpp
create mode 100644 src/citeme.h
create mode 100644 src/cohesion_model_sjkr.h
create mode 100644 src/cohesion_model_sjkr2.h
create mode 100644 src/compute_erotate_rigid.cpp
create mode 100644 src/compute_erotate_rigid.h
create mode 100644 src/compute_erotate_sphere_atom.cpp
create mode 100644 src/compute_erotate_sphere_atom.h
create mode 100644 src/compute_inertia_molecule.cpp
create mode 100644 src/compute_inertia_molecule.h
create mode 100644 src/compute_ke_rigid.cpp
create mode 100644 src/compute_ke_rigid.h
delete mode 100644 src/compute_ti.cpp
delete mode 100644 src/compute_ti.h
create mode 100644 src/compute_vacf.cpp
create mode 100644 src/compute_vacf.h
create mode 100644 src/contact_interface.h
create mode 100644 src/contact_model_constants.h
create mode 100644 src/contact_models.h
create mode 100644 src/dihedral_hybrid.cpp
create mode 100644 src/dihedral_hybrid.h
create mode 100644 src/dump_movie.cpp
create mode 100644 src/dump_movie.h
delete mode 100644 src/fix_contact_history_I.h
create mode 100644 src/fix_contact_history_mesh.cpp
create mode 100644 src/fix_contact_history_mesh.h
create mode 100644 src/fix_contact_history_mesh_I.h
delete mode 100644 src/fix_efield.cpp
delete mode 100644 src/fix_efield.h
delete mode 100644 src/fix_evaporate.cpp
delete mode 100644 src/fix_orient_fcc.cpp
create mode 100644 src/fix_rigid_nh.cpp
create mode 100644 src/fix_rigid_nh.h
create mode 100644 src/fix_rigid_nph.cpp
create mode 100644 src/fix_rigid_nph.h
create mode 100644 src/fix_rigid_npt.cpp
create mode 100644 src/fix_rigid_npt.h
create mode 100644 src/fix_rigid_small.cpp
create mode 100644 src/fix_rigid_small.h
create mode 100644 src/fix_store.cpp
create mode 100644 src/fix_store.h
delete mode 100644 src/fix_thermal_conductivity.cpp
delete mode 100644 src/fix_ttm.cpp
delete mode 100644 src/fix_viscosity.cpp
create mode 100644 src/fix_wall_gran_base.h
delete mode 100644 src/fix_wall_gran_hertz_history.cpp
delete mode 100644 src/fix_wall_gran_hertz_history.h
delete mode 100644 src/fix_wall_gran_hertz_history_simple.cpp
delete mode 100644 src/fix_wall_gran_hertz_history_simple.h
delete mode 100644 src/fix_wall_gran_hooke.cpp
delete mode 100644 src/fix_wall_gran_hooke.h
delete mode 100644 src/fix_wall_gran_hooke_history.cpp
delete mode 100644 src/fix_wall_gran_hooke_history.h
delete mode 100644 src/fix_wall_gran_hooke_history_simple.cpp
delete mode 100644 src/fix_wall_gran_hooke_history_simple.h
delete mode 100644 src/fix_wall_gran_hooke_simple.cpp
delete mode 100644 src/fix_wall_gran_hooke_simple.h
create mode 100644 src/fix_wall_lj1043.cpp
create mode 100644 src/fix_wall_lj1043.h
create mode 100644 src/global_properties.cpp
create mode 100644 src/global_properties.h
create mode 100644 src/improper_hybrid.cpp
create mode 100644 src/improper_hybrid.h
create mode 100644 src/math_complex.h
create mode 100644 src/math_special.h
create mode 100644 src/math_vector.h
create mode 100644 src/my_page.h
create mode 100644 src/my_pool_chunk.h
create mode 100644 src/normal_model_hertz.h
create mode 100644 src/normal_model_hertz_stiffness.h
create mode 100644 src/normal_model_hooke.h
create mode 100644 src/normal_model_hooke_hysteresis.h
create mode 100644 src/normal_model_hooke_stiffness.h
create mode 100644 src/os_specific.h
create mode 100644 src/pair_coul_dsf.cpp
create mode 100644 src/pair_coul_dsf.h
create mode 100644 src/pair_gran_base.h
delete mode 100644 src/pair_gran_hertz_history.cpp
delete mode 100644 src/pair_gran_hertz_history.h
delete mode 100644 src/pair_gran_hertz_history_simple.cpp
delete mode 100644 src/pair_gran_hertz_history_simple.h
delete mode 100644 src/pair_gran_hooke.h
delete mode 100644 src/pair_gran_hooke_history.h
delete mode 100644 src/pair_gran_hooke_history_hysteresis.cpp
delete mode 100644 src/pair_gran_hooke_history_hysteresis.h
delete mode 100644 src/pair_gran_hooke_history_simple.cpp
delete mode 100644 src/pair_gran_hooke_history_simple.h
delete mode 100644 src/pair_gran_hooke_simple.cpp
delete mode 100644 src/pair_gran_hooke_simple.h
create mode 100644 src/pair_lj_cut_coul_dsf.cpp
create mode 100644 src/pair_lj_cut_coul_dsf.h
create mode 100644 src/pair_mie_cut.cpp
create mode 100644 src/pair_mie_cut.h
create mode 100644 src/pair_zbl.cpp
create mode 100644 src/pair_zbl.h
create mode 100644 src/property_registry.cpp
create mode 100644 src/property_registry.h
create mode 100644 src/read_dump.cpp
create mode 100644 src/read_dump.h
create mode 100644 src/reader.cpp
create mode 100644 src/reader.h
create mode 100644 src/reader_native.cpp
create mode 100644 src/reader_native.h
create mode 100644 src/reader_xyz.cpp
create mode 100644 src/reader_xyz.h
create mode 100644 src/rerun.cpp
create mode 100644 src/rerun.h
create mode 100644 src/rolling_model_cdt.h
create mode 100644 src/rolling_model_epsd.h
create mode 100644 src/rolling_model_epsd2.h
create mode 100644 src/settings.h
copy doc/fix_wall_region_sph.html => src/style_body.h (100%)
create mode 100644 src/style_cohesion_model.h
copy doc/fix_wall_region_sph.html => src/style_contact_model.blacklist (100%)
create mode 100644 src/style_contact_model.h
create mode 100644 src/style_normal_model.h
create mode 100644 src/style_reader.h
create mode 100644 src/style_rolling_model.h
create mode 100644 src/style_surface_model.h
create mode 100644 src/style_tangential_model.h
create mode 100644 src/surface_model_default.h
create mode 100644 src/tangential_model_history.h
create mode 100644 src/tangential_model_no_history.h
create mode 100644 src/write_data.cpp
create mode 100644 src/write_data.h
create mode 100644 src/write_dump.cpp
create mode 100644 src/write_dump.h
delete mode 120000 tools/ch2lmp/example/1ac7_trj.psf
create mode 100755 tools/kate/README.txt
create mode 100755 tools/kate/lammps.xml
create mode 100755 tools/moltemplate/LICENSE.TXT
create mode 100755 tools/moltemplate/README.TXT
create mode 100755 tools/moltemplate/common/amber/README.TXT
create mode 100755 tools/moltemplate/common/amber/amberparm2lt.sh
create mode 100755 tools/moltemplate/common/amber/amberparm_angle_to_lt.py
create mode 100755 tools/moltemplate/common/amber/amberparm_bond_to_lt.py
create mode 100755 tools/moltemplate/common/amber/amberparm_dihedral_to_lt.py
create mode 100755 tools/moltemplate/common/amber/amberparm_improper_to_lt.py
create mode 100755 tools/moltemplate/common/amber/amberparm_mass_to_lt.py
create mode 100755 tools/moltemplate/common/amber/amberparm_pair_to_lt.py
create mode 100755 tools/moltemplate/common/gaff.lt
create mode 100755 tools/moltemplate/common/graphene.lt
create mode 100755 tools/moltemplate/common/images/graphene_unit_cell.jpg
create mode 100755 tools/moltemplate/common/images/ice_rect8_unitcell.png
create mode 100755 tools/moltemplate/common/images/spce_ball_and_stick.jpg
create mode 100755 tools/moltemplate/common/spce.lt
create mode 100755 tools/moltemplate/common/spce_ice_rect8.lt
create mode 100755 tools/moltemplate/common/tip3p_1983.lt
create mode 100755 tools/moltemplate/common/tip3p_2004.lt
create mode 100755 tools/moltemplate/common/trappe1998.lt
create mode 100755 tools/moltemplate/common/watmw.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README.TXT
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DLPC.xyz
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/DPPC.xyz
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/protein.xyz
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min
create mode 100755 tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/README.TXT
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/walls+solvent+polymer_t=0.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/run.in.npt
create mode 100755 tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
create mode 100755 tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
create mode 100755 tools/moltemplate/examples/README.TXT
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
create mode 100755 tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt
create mode 100755 tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt
create mode 100755 tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/graphene_unit_cell.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/images/water_side_nopbc_LR.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
create mode 100755 tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt
copy doc/fix_wall_region_sph.html => tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 (100%)
mode change 100644 => 100755
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
create mode 100755 tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/wat.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/ions.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
create mode 100755 tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in
create mode 100755 tools/moltemplate/examples/silly/sierpinski/README.TXT
create mode 100755 tools/moltemplate/examples/silly/sierpinski/README_setup.sh
create mode 100755 tools/moltemplate/examples/silly/sierpinski/README_visualize.txt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg
create mode 100755 tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg
create mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt
create mode 100755 tools/moltemplate/examples/silly/sierpinski/run.in
create mode 100755 tools/moltemplate/moltemplate_manual.pdf
create mode 100755 tools/moltemplate/src/bonds_by_type.py
create mode 100755 tools/moltemplate/src/dump2data.py
create mode 100755 tools/moltemplate/src/extract_lammps_data.py
create mode 100755 tools/moltemplate/src/ltemplify.py
create mode 100755 tools/moltemplate/src/lttree.py
create mode 100755 tools/moltemplate/src/lttree_check.py
create mode 100755 tools/moltemplate/src/lttree_postprocess.py
create mode 100755 tools/moltemplate/src/lttree_styles.py
create mode 100755 tools/moltemplate/src/moltemplate.sh
create mode 100755 tools/moltemplate/src/nbody_Angles.py
create mode 100755 tools/moltemplate/src/nbody_Bonds.py
create mode 100755 tools/moltemplate/src/nbody_Dihedrals.py
create mode 100755 tools/moltemplate/src/nbody_Impropers.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILnoswap.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJK.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJKL.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLnoswap.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIK.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIKL.py
create mode 100755 tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapJK.py
create mode 100755 tools/moltemplate/src/nbody_by_type.py
create mode 100755 tools/moltemplate/src/nbody_by_type_lib.py
create mode 100755 tools/moltemplate/src/nbody_by_type_lib_old.py
create mode 100755 tools/moltemplate/src/nbody_fix_ttree_assignments.py
create mode 100755 tools/moltemplate/src/nbody_graph_search.py
create mode 100755 tools/moltemplate/src/nbody_reorder_atoms.py
create mode 100755 tools/moltemplate/src/ordereddict.py
create mode 100755 tools/moltemplate/src/pdbsort.py
create mode 100755 tools/moltemplate/src/postprocess_input_script.py
create mode 100755 tools/moltemplate/src/raw2data.py
create mode 100755 tools/moltemplate/src/remove_duplicate_atoms.py
create mode 100755 tools/moltemplate/src/remove_duplicates_nbody.py
create mode 100755 tools/moltemplate/src/renumber_DATA_first_column.py
create mode 100755 tools/moltemplate/src/ttree.py
create mode 100755 tools/moltemplate/src/ttree_lex.py
create mode 100755 tools/moltemplate/src/ttree_matrix_stack.py
create mode 100755 tools/moltemplate/src/ttree_render.py
delete mode 100755 tools/msi2lmp/TriclinicModification.pdf
delete mode 100755 tools/msi2lmp/biosym_frc_files/README
delete mode 100755 tools/msi2lmp/biosym_frc_files/pcff.frc
create mode 100755 tools/msi2lmp/frc_files/README
rename tools/msi2lmp/{biosym_frc_files => frc_files}/cff91.frc (100%)
rename tools/msi2lmp/{biosym_frc_files => frc_files}/clayff.frc (100%)
create mode 100755 tools/msi2lmp/frc_files/compass_published.frc
rename tools/msi2lmp/{biosym_frc_files => frc_files}/cvff.frc (100%)
rename tools/msi2lmp/{biosym_frc_files => frc_files}/cvff_aug.frc (100%)
create mode 100755 tools/msi2lmp/frc_files/oplsaa.frc
create mode 100755 tools/msi2lmp/frc_files/pcff.frc
rename tools/msi2lmp/{biosym_frc_files => frc_files}/pcff.rlb (100%)
rename tools/msi2lmp/{biosym_frc_files => frc_files}/pcff_templates.dat (100%)
delete mode 100755 tools/msi2lmp/src/Msi2LMP2.h
delete mode 100755 tools/msi2lmp/src/WriteDataFile01.c
delete mode 100755 tools/msi2lmp/src/WriteDataFile05.c
create mode 100755 tools/msi2lmp/src/msi2lmp.h
create mode 100755 tools/msi2lmp/test/PyAC_bulk-clayff.car
create mode 100755 tools/msi2lmp/test/PyAC_bulk-clayff.mdf
create mode 100755 tools/msi2lmp/test/benzene-class1.car
create mode 100755 tools/msi2lmp/test/benzene-class1.mdf
create mode 100755 tools/msi2lmp/test/benzene-class2a.car
create mode 100755 tools/msi2lmp/test/benzene-class2a.mdf
create mode 100755 tools/msi2lmp/test/benzene-class2b.car
create mode 100755 tools/msi2lmp/test/benzene-class2b.mdf
delete mode 100755 tools/msi2lmp/test/correct/data.crambin
delete mode 100755 tools/msi2lmp/test/correct/data.nylon
delete mode 100755 tools/msi2lmp/test/correct/data.phen3_cff97
rename tools/msi2lmp/test/{crambin.car => crambin-class1.car} (100%)
rename tools/msi2lmp/test/{crambin.mdf => crambin-class1.mdf} (100%)
create mode 100755 tools/msi2lmp/test/data-compare.pl
create mode 100755 tools/msi2lmp/test/ethane-class1.car
create mode 100755 tools/msi2lmp/test/ethane-class1.mdf
create mode 100755 tools/msi2lmp/test/ethane-class2a.car
create mode 100755 tools/msi2lmp/test/ethane-class2a.mdf
create mode 100755 tools/msi2lmp/test/ethane-class2b.car
create mode 100755 tools/msi2lmp/test/ethane-class2b.mdf
create mode 100755 tools/msi2lmp/test/ethane-oplsaa.car
create mode 100755 tools/msi2lmp/test/ethane-oplsaa.mdf
create mode 100755 tools/msi2lmp/test/h2-h2o-class1.car
create mode 100755 tools/msi2lmp/test/h2-h2o-class1.mdf
create mode 100755 tools/msi2lmp/test/h2-h2o-class2b.car
create mode 100755 tools/msi2lmp/test/h2-h2o-class2b.mdf
create mode 100755 tools/msi2lmp/test/hap_crystal-class1.car
create mode 100755 tools/msi2lmp/test/hap_crystal-class1.mdf
create mode 100755 tools/msi2lmp/test/hap_crystal-class2b.car
create mode 100755 tools/msi2lmp/test/hap_crystal-class2b.mdf
create mode 100755 tools/msi2lmp/test/hydrogen-class1.car
create mode 100755 tools/msi2lmp/test/hydrogen-class1.mdf
create mode 100755 tools/msi2lmp/test/hydrogen-class2a.car
create mode 100755 tools/msi2lmp/test/hydrogen-class2a.mdf
create mode 100755 tools/msi2lmp/test/in.PyAC_bulk-clayff
create mode 100755 tools/msi2lmp/test/in.benzene-class1
create mode 100755 tools/msi2lmp/test/in.benzene-class2a
create mode 100755 tools/msi2lmp/test/in.benzene-class2b
create mode 100755 tools/msi2lmp/test/in.crambin-class1
create mode 100755 tools/msi2lmp/test/in.ethane-class1
create mode 100755 tools/msi2lmp/test/in.ethane-class2a
create mode 100755 tools/msi2lmp/test/in.ethane-class2b
create mode 100755 tools/msi2lmp/test/in.ethane-oplsaa
create mode 100755 tools/msi2lmp/test/in.h2-h2o-class1
create mode 100755 tools/msi2lmp/test/in.h2-h2o-class2b
create mode 100755 tools/msi2lmp/test/in.hap_crystal-class1
create mode 100755 tools/msi2lmp/test/in.hap_crystal-class2b
create mode 100755 tools/msi2lmp/test/in.hydrogen-class1
create mode 100755 tools/msi2lmp/test/in.hydrogen-class2a
create mode 100755 tools/msi2lmp/test/in.naphthalene-class1
create mode 100755 tools/msi2lmp/test/in.naphthalene-class2a
create mode 100755 tools/msi2lmp/test/in.naphthalene-class2b
create mode 100755 tools/msi2lmp/test/in.nylon-class1
create mode 100755 tools/msi2lmp/test/in.phen3_cff97-class1
create mode 100755 tools/msi2lmp/test/in.water-class1
create mode 100755 tools/msi2lmp/test/in.water-class2b
create mode 100755 tools/msi2lmp/test/naphthalene-class1.car
create mode 100755 tools/msi2lmp/test/naphthalene-class1.mdf
create mode 100755 tools/msi2lmp/test/naphthalene-class2a.car
create mode 100755 tools/msi2lmp/test/naphthalene-class2a.mdf
create mode 100755 tools/msi2lmp/test/naphthalene-class2b.car
create mode 100755 tools/msi2lmp/test/naphthalene-class2b.mdf
rename tools/msi2lmp/test/{nylon.car => nylon-class1.car} (100%)
rename tools/msi2lmp/test/{nylon.mdf => nylon-class1.mdf} (100%)
rename tools/msi2lmp/test/{phen3_cff97.car => phen3_cff97-class1.car} (100%)
rename tools/msi2lmp/test/{phen3_cff97.mdf => phen3_cff97-class1.mdf} (100%)
create mode 100755 tools/msi2lmp/test/reference/PyAC_bulk-clayff.data
create mode 100755 tools/msi2lmp/test/reference/PyAC_bulk-clayff.data2
create mode 100755 tools/msi2lmp/test/reference/benzene-class1.data
create mode 100755 tools/msi2lmp/test/reference/benzene-class1.data2
create mode 100755 tools/msi2lmp/test/reference/benzene-class1.data3
create mode 100755 tools/msi2lmp/test/reference/benzene-class2a.data
create mode 100755 tools/msi2lmp/test/reference/benzene-class2a.data2
create mode 100755 tools/msi2lmp/test/reference/benzene-class2b.data
create mode 100755 tools/msi2lmp/test/reference/benzene-class2b.data2
create mode 100755 tools/msi2lmp/test/reference/crambin-class1.data
create mode 100755 tools/msi2lmp/test/reference/crambin-class1.data2
create mode 100755 tools/msi2lmp/test/reference/ethane-class1.data
create mode 100755 tools/msi2lmp/test/reference/ethane-class1.data2
create mode 100755 tools/msi2lmp/test/reference/ethane-class2a.data
create mode 100755 tools/msi2lmp/test/reference/ethane-class2a.data2
create mode 100755 tools/msi2lmp/test/reference/ethane-class2b.data
create mode 100755 tools/msi2lmp/test/reference/ethane-class2b.data2
create mode 100755 tools/msi2lmp/test/reference/ethane-oplsaa.data
create mode 100755 tools/msi2lmp/test/reference/ethane-oplsaa.data2
create mode 100755 tools/msi2lmp/test/reference/h2-h2o-class1.data
create mode 100755 tools/msi2lmp/test/reference/h2-h2o-class1.data2
create mode 100755 tools/msi2lmp/test/reference/h2-h2o-class2b.data
create mode 100755 tools/msi2lmp/test/reference/h2-h2o-class2b.data2
create mode 100755 tools/msi2lmp/test/reference/hap_crystal-class1.data
create mode 100755 tools/msi2lmp/test/reference/hap_crystal-class1.data2
create mode 100755 tools/msi2lmp/test/reference/hap_crystal-class2b.data
create mode 100755 tools/msi2lmp/test/reference/hap_crystal-class2b.data2
create mode 100755 tools/msi2lmp/test/reference/hydrogen-class1.data
create mode 100755 tools/msi2lmp/test/reference/hydrogen-class1.data2
create mode 100755 tools/msi2lmp/test/reference/hydrogen-class2a.data
create mode 100755 tools/msi2lmp/test/reference/hydrogen-class2a.data2
create mode 100755 tools/msi2lmp/test/reference/naphthalene-class1.data
create mode 100755 tools/msi2lmp/test/reference/naphthalene-class1.data2
create mode 100755 tools/msi2lmp/test/reference/naphthalene-class2a.data
create mode 100755 tools/msi2lmp/test/reference/naphthalene-class2a.data2
create mode 100755 tools/msi2lmp/test/reference/naphthalene-class2b.data
create mode 100755 tools/msi2lmp/test/reference/naphthalene-class2b.data2
create mode 100755 tools/msi2lmp/test/reference/nylon-class1.data
create mode 100755 tools/msi2lmp/test/reference/nylon-class1.data2
create mode 100755 tools/msi2lmp/test/reference/phen3_cff97-class1.data
create mode 100755 tools/msi2lmp/test/reference/phen3_cff97-class1.data2
create mode 100755 tools/msi2lmp/test/reference/water-class1.data
create mode 100755 tools/msi2lmp/test/reference/water-class1.data2
create mode 100755 tools/msi2lmp/test/reference/water-class2b.data
create mode 100755 tools/msi2lmp/test/reference/water-class2b.data2
create mode 100755 tools/msi2lmp/test/runtests.sh
create mode 100755 tools/msi2lmp/test/water-class1.car
create mode 100755 tools/msi2lmp/test/water-class1.mdf
create mode 100755 tools/msi2lmp/test/water-class2b.car
create mode 100755 tools/msi2lmp/test/water-class2b.mdf
create mode 100755 tools/phonon/Makefile
create mode 100755 tools/phonon/README
create mode 100755 tools/phonon/dynmat.cpp
create mode 100755 tools/phonon/dynmat.h
create mode 100755 tools/phonon/green.cpp
create mode 100755 tools/phonon/green.h
create mode 100755 tools/phonon/interpolate.cpp
create mode 100755 tools/phonon/interpolate.h
create mode 100755 tools/phonon/main.cpp
create mode 100755 tools/phonon/memory.cpp
create mode 100755 tools/phonon/memory.h
create mode 100755 tools/phonon/phonon.cpp
create mode 100755 tools/phonon/phonon.h
create mode 100755 tools/phonon/timer.cpp
create mode 100755 tools/phonon/timer.h
create mode 100755 tools/phonon/version.h
create mode 100755 tools/polybond/Manual.pdf
create mode 100755 tools/polybond/README
create mode 100755 tools/polybond/lmpsdata.py
mode change 100755 => 100644 tools/restart2data.cpp
delete mode 100755 tools/thermo_extract.c
create mode 100755 tools/xmgrace/README
create mode 100755 tools/xmgrace/lammpsplot.cpp
create mode 100755 tools/xmgrace/lammpsplot.pdf
create mode 100755 tools/xmgrace/logplotawk.oneliner
create mode 100755 tools/xmgrace/logplotgrep.oneliner
create mode 100755 tools/xmgrace/plotthermodata.awk
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/liggghts.git
More information about the debian-science-commits
mailing list