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Axel Kohlmeyer 09c19a936b update URLs in source code and manual
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ASPHERE
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BODY
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CLASS2
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COMPRESS
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CORESHELL
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DEPEND
add clang-format support for fastdep tool
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DIPOLE
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fmt
apply clang-format to all headers with some exceptions
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GPU
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GRANULAR
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KIM
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KOKKOS
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KSPACE
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LATTE
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MAKE
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MANYBODY
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MC
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MESSAGE
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MISC
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MLIAP
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MOLECULE
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OPT
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PERI
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PLUGIN
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POEMS
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PYTHON
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QEQ
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REPLICA
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USER-ADIOS
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USER-QUIP
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USER-REACTION
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USER-YAFF
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VORONOI
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.clang-format
switch to 100 chars columnwidth and apply clang-format to a few .cpp files
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.gitignore
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accelerator_kokkos.h
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accelerator_omp.h
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angle_deprecated.cpp
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angle_deprecated.h
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angle_hybrid.cpp
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angle_hybrid.h
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angle_zero.cpp
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angle_zero.h
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angle.cpp
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angle.h
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arg_info.cpp
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arg_info.h
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atom_map.cpp
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atom_map.h
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atom_masks.h
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atom_vec_atomic.cpp
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atom_vec_atomic.h
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atom_vec_body.cpp
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atom_vec_body.h
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atom_vec_charge.cpp
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atom_vec_charge.h
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atom_vec_ellipsoid.cpp
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atom_vec_ellipsoid.h
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atom_vec_hybrid.cpp
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atom_vec_hybrid.h
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atom_vec_line.cpp
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atom_vec_line.h
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atom_vec_sphere.cpp
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atom_vec_sphere.h
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atom_vec_tri.cpp
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atom_vec_tri.h
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atom_vec.cpp
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atom_vec.h
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atom.cpp
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atom.h
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balance.cpp
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balance.h
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body.cpp
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body.h
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bond_deprecated.cpp
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bond_deprecated.h
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bond_hybrid.cpp
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bond_hybrid.h
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bond_zero.cpp
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bond_zero.h
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bond.cpp
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bond.h
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change_box.cpp
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change_box.h
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citeme.cpp
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citeme.h
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comm_brick.cpp
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comm_brick.h
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comm_tiled.cpp
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comm_tiled.h
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comm.cpp
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comm.h
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command.h
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compute_adf.cpp
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compute_adf.h
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compute_aggregate_atom.cpp
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compute_aggregate_atom.h
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compute_angle_local.cpp
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compute_angle_local.h
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compute_angle.cpp
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compute_angle.h
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compute_angmom_chunk.cpp
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compute_angmom_chunk.h
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compute_bond_local.cpp
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compute_bond_local.h
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compute_bond.cpp
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compute_bond.h
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compute_centro_atom.cpp
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compute_centro_atom.h
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compute_centroid_stress_atom.cpp
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compute_centroid_stress_atom.h
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compute_chunk_atom.cpp
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compute_chunk_atom.h
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compute_chunk_spread_atom.cpp
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compute_chunk_spread_atom.h
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compute_cluster_atom.cpp
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compute_cluster_atom.h
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compute_cna_atom.cpp
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compute_cna_atom.h
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compute_com_chunk.cpp
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compute_com_chunk.h
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compute_com.cpp
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compute_com.h
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compute_contact_atom.cpp
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compute_contact_atom.h
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compute_coord_atom.cpp
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compute_coord_atom.h
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compute_deprecated.cpp
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compute_deprecated.h
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compute_dihedral_local.cpp
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compute_dihedral_local.h
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compute_dihedral.cpp
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compute_dihedral.h
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compute_dipole_chunk.cpp
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compute_dipole_chunk.h
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compute_displace_atom.cpp
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compute_displace_atom.h
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compute_erotate_sphere_atom.cpp
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compute_erotate_sphere_atom.h
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compute_erotate_sphere.cpp
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compute_erotate_sphere.h
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compute_fragment_atom.cpp
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compute_fragment_atom.h
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compute_global_atom.cpp
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compute_global_atom.h
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compute_group_group.cpp
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compute_group_group.h
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compute_gyration_chunk.cpp
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compute_gyration_chunk.h
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compute_gyration.cpp
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compute_gyration.h
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compute_heat_flux.cpp
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compute_heat_flux.h
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compute_hexorder_atom.cpp
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compute_hexorder_atom.h
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compute_improper_local.cpp
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compute_improper_local.h
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compute_improper.cpp
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compute_improper.h
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compute_inertia_chunk.cpp
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compute_inertia_chunk.h
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compute_ke_atom.cpp
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compute_ke_atom.h
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compute_ke.cpp
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compute_ke.h
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compute_msd_chunk.cpp
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compute_msd_chunk.h
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compute_msd.cpp
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compute_msd.h
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compute_omega_chunk.cpp
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compute_omega_chunk.h
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compute_orientorder_atom.cpp
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compute_orientorder_atom.h
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compute_pair_local.cpp
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compute_pair_local.h
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compute_pair.cpp
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compute_pair.h
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compute_pe_atom.cpp
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compute_pe_atom.h
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compute_pe.cpp
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compute_pe.h
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compute_pressure.cpp
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compute_pressure.h
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compute_property_atom.cpp
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compute_property_atom.h
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compute_property_chunk.cpp
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compute_property_chunk.h
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compute_property_local.cpp
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compute_property_local.h
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compute_rdf.cpp
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compute_rdf.h
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compute_reduce_chunk.cpp
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compute_reduce_region.cpp
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compute_reduce_region.h
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compute_reduce.cpp
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compute_reduce.h
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compute_slice.cpp
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compute_slice.h
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compute_stress_atom.cpp
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compute_stress_atom.h
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compute_temp_chunk.cpp
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compute_temp_chunk.h
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compute_temp_com.cpp
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compute_temp_com.h
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compute_temp_deform.cpp
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compute_temp_deform.h
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compute_temp_partial.cpp
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compute_temp_partial.h
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compute_temp_profile.cpp
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compute_temp_profile.h
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compute_temp_ramp.cpp
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compute_temp_ramp.h
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compute_temp_region.cpp
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compute_temp_region.h
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compute_temp_sphere.cpp
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compute_temp_sphere.h
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compute_temp.cpp
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compute_temp.h
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compute_torque_chunk.cpp
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compute_torque_chunk.h
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compute_vacf.cpp
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compute_vacf.h
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compute_vcm_chunk.cpp
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compute_vcm_chunk.h
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compute.cpp
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compute.h
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create_atoms.cpp
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create_atoms.h
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create_bonds.cpp
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create_bonds.h
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create_box.cpp
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create_box.h
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delete_atoms.cpp
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delete_atoms.h
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delete_bonds.cpp
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delete_bonds.h
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Depend.sh
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deprecated.cpp
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deprecated.h
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dihedral_deprecated.cpp
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dihedral_deprecated.h
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dihedral_hybrid.cpp
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dihedral_hybrid.h
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dihedral_zero.cpp
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dihedral_zero.h
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dihedral.cpp
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dihedral.h
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displace_atoms.cpp
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displace_atoms.h
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domain.cpp
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domain.h
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dump_atom.cpp
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dump_atom.h
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dump_cfg.cpp
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dump_cfg.h
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dump_custom.cpp
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dump_custom.h
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dump_dcd.cpp
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dump_dcd.h
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dump_deprecated.cpp
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dump_deprecated.h
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dump_image.cpp
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dump_image.h
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dump_local.cpp
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dump_local.h
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dump_movie.cpp
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dump_movie.h
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dump_xyz.cpp
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dump_xyz.h
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dump.cpp
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dump.h
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error.cpp
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error.h
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exceptions.h
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Fetch.sh
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file_writer.h
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finish.cpp
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finish.h
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fix_adapt.h
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fix_addforce.h
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fix_ave_atom.cpp
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fix_ave_atom.h
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fix_ave_chunk.h
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fix_ave_correlate.h
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fix_ave_time.h
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fix_aveforce.cpp
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fix_aveforce.h
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fix_balance.h
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fix_box_relax.cpp
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fix_box_relax.h
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fix_gravity.h
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fix_neigh_history.cpp
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fix_nh_sphere.cpp
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fix_nh_sphere.h
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fix_nh.cpp
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fix_nh.h
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fix_nph_sphere.cpp
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fix_nph_sphere.h
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fix_nph.cpp
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fix_nph.h
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fix_npt_sphere.cpp
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fix_npt_sphere.h
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fix_npt.cpp
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fix_npt.h
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fix_numdiff.h
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fix_nve_limit.cpp
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fix_nve_limit.h
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fix_nve_noforce.cpp
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fix_nve_noforce.h
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fix_nve_sphere.cpp
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fix_nve_sphere.h
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fix_nve.cpp
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fix_nve.h
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fix_nvt_sllod.cpp
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fix_nvt_sllod.h
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fix_nvt_sphere.cpp
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fix_nvt_sphere.h
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fix_nvt.cpp
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fix_nvt.h
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fix_planeforce.cpp
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fix_planeforce.h
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fix_press_berendsen.cpp
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fix_press_berendsen.h
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fix_print.cpp
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fix_print.h
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fix_property_atom.cpp
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fix_property_atom.h
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fix_read_restart.cpp
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fix_read_restart.h
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fix_recenter.cpp
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fix_recenter.h
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fix_respa.cpp
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fix_respa.h
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fix_restrain.cpp
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fix_restrain.h
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fix_setforce.cpp
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fix_setforce.h
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fix_spring_chunk.cpp
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fix_spring_chunk.h
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fix_spring_self.h
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fix_spring.cpp
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fix_spring.h
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fix_store_force.cpp
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fix_store_force.h
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fix_store_state.h
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fix_store.cpp
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fix_store.h
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fix_temp_berendsen.cpp
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fix_temp_berendsen.h
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fix_temp_csld.cpp
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fix_temp_csld.h
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fix_temp_csvr.cpp
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fix_temp_csvr.h
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fix_temp_rescale.cpp
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fix_temp_rescale.h
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fix_tmd.cpp
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fix_tmd.h
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fix_vector.cpp
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fix_vector.h
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fix_viscous.cpp
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fix_viscous.h
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fix_wall_harmonic.cpp
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fix_wall_harmonic.h
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fix_wall_lj93.cpp
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fix_wall_lj93.h
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fix_wall_lj126.cpp
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fix_wall_lj126.h
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fix_wall_lj1043.cpp
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fix_wall_lj1043.h
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fix_wall_morse.cpp
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fix_wall_morse.h
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fix_wall_reflect.cpp
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fix_wall_reflect.h
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fix_wall_region.cpp
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fix_wall_region.h
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fix_wall.cpp
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fix_wall.h
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fix.cpp
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force.cpp
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Install.sh
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library.cpp
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library.h
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main.cpp
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Make.sh
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Makefile
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math_const.h
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math_special.h
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memory.cpp
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memory.h
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min.h
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molecule.h
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mpiio.h
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nbin.h
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neighbor.h
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npair_full_bin_atomonly.cpp
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npair_full_bin_atomonly.h
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npair_full_bin_ghost.h
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npair_full_bin.h
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npair_full_multi_old.h
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npair_full_multi.h
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npair_full_nsq_ghost.cpp
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npair_full_nsq_ghost.h
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npair_full_nsq.cpp
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npair_full_nsq.h
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npair_half_bin_atomonly_newton.cpp
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npair_half_bin_atomonly_newton.h
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npair_half_bin_newtoff_ghost.cpp
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npair_half_bin_newtoff_ghost.h
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npair_half_bin_newtoff.cpp
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npair_half_bin_newtoff.h
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npair_half_bin_newton_tri.cpp
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npair_half_bin_newton_tri.h
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npair_half_bin_newton.cpp
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npair_half_bin_newton.h
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npair_half_multi_newtoff.cpp
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npair_half_multi_newtoff.h
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npair_half_multi_newton_tri.cpp
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npair_half_multi_newton_tri.h
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npair_half_multi_newton.cpp
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npair_half_multi_newton.h
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npair_half_multi_old_newtoff.cpp
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npair_half_multi_old_newtoff.h
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npair_half_multi_old_newton_tri.cpp
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npair_half_multi_old_newton_tri.h
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npair_half_multi_old_newton.cpp
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npair_half_multi_old_newton.h
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npair_half_nsq_newtoff_ghost.cpp
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npair_half_nsq_newtoff_ghost.h
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npair_half_nsq_newtoff.cpp
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npair_half_nsq_newtoff.h
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npair_half_nsq_newton.cpp
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npair_half_nsq_newton.h
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npair_half_respa_bin_newtoff.cpp
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npair_half_respa_bin_newtoff.h
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npair_half_respa_bin_newton_tri.cpp
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npair_half_respa_bin_newton_tri.h
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npair_half_respa_bin_newton.cpp
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npair_half_respa_bin_newton.h
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npair_half_respa_nsq_newtoff.cpp
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npair_half_respa_nsq_newtoff.h
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npair_half_respa_nsq_newton.cpp
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npair_half_respa_nsq_newton.h
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npair_half_size_bin_newtoff.cpp
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npair_half_size_bin_newtoff.h
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npair_half_size_bin_newton_tri.cpp
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npair_half_size_bin_newton_tri.h
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npair_half_size_bin_newton.cpp
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npair_half_size_bin_newton.h
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npair_half_size_multi_newtoff.cpp
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npair_half_size_multi_newtoff.h
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npair_half_size_multi_newton_tri.cpp
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npair_half_size_multi_newton_tri.h
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npair_half_size_multi_newton.cpp
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npair_half_size_multi_newton.h
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npair_half_size_multi_old_newtoff.cpp
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npair_half_size_multi_old_newtoff.h
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npair_half_size_multi_old_newton_tri.cpp
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npair_half_size_multi_old_newton_tri.h
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npair_half_size_multi_old_newton.cpp
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npair_half_size_multi_old_newton.h
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npair_half_size_nsq_newtoff.cpp
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npair_half_size_nsq_newtoff.h
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npair_half_size_nsq_newton.cpp
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npair_half_size_nsq_newton.h
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npair_halffull_newtoff.cpp
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npair_halffull_newtoff.h
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npair_halffull_newton.cpp
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npair_halffull_newton.h
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npair_skip_respa.cpp
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npair_skip_respa.h
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npair_skip_size_off2on_oneside.cpp
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npair_skip_size_off2on_oneside.h
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npair_skip_size_off2on.cpp
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npair_skip_size_off2on.h
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npair_skip_size.cpp
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npair_skip_size.h
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npair_skip.cpp
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npair_skip.h
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npair.cpp
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npair.h
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nstencil_full_bin_2d.cpp
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nstencil_full_bin_2d.h
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nstencil_full_bin_3d.cpp
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nstencil_full_bin_3d.h
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nstencil_full_ghost_bin_2d.cpp
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nstencil_full_ghost_bin_2d.h
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nstencil_full_ghost_bin_3d.cpp
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nstencil_full_ghost_bin_3d.h
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nstencil_full_multi_2d.cpp
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nstencil_full_multi_2d.h
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nstencil_full_multi_3d.cpp
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nstencil_full_multi_3d.h
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nstencil_full_multi_old_2d.cpp
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nstencil_full_multi_old_2d.h
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nstencil_full_multi_old_3d.cpp
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nstencil_full_multi_old_3d.h
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nstencil_half_bin_2d_tri.cpp
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nstencil_half_bin_2d_tri.h
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nstencil_half_bin_2d.cpp
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nstencil_half_bin_2d.h
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nstencil_half_bin_3d_tri.cpp
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nstencil_half_bin_3d_tri.h
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nstencil_half_bin_3d.cpp
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nstencil_half_bin_3d.h
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nstencil_half_multi_2d_tri.cpp
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nstencil_half_multi_2d_tri.h
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nstencil_half_multi_2d.cpp
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nstencil_half_multi_2d.h
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nstencil_half_multi_3d_tri.cpp
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nstencil_half_multi_3d_tri.h
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nstencil_half_multi_3d.cpp
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nstencil_half_multi_3d.h
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nstencil_half_multi_old_2d_tri.cpp
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nstencil_half_multi_old_2d_tri.h
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nstencil_half_multi_old_2d.cpp
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nstencil_half_multi_old_2d.h
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nstencil_half_multi_old_3d_tri.cpp
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nstencil_half_multi_old_3d_tri.h
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nstencil_half_multi_old_3d.cpp
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nstencil_half_multi_old_3d.h
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nstencil.cpp
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nstencil.h
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ntopo_angle_all.cpp
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ntopo_angle_all.h
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ntopo_angle_partial.cpp
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ntopo_angle_partial.h
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ntopo_angle_template.cpp
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ntopo_angle_template.h
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ntopo_bond_all.cpp
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ntopo_bond_all.h
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ntopo_bond_partial.cpp
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ntopo_bond_partial.h
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ntopo_bond_template.cpp
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ntopo_bond_template.h
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ntopo_dihedral_all.cpp
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ntopo_dihedral_all.h
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ntopo_dihedral_partial.cpp
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ntopo_dihedral_partial.h
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ntopo_dihedral_template.cpp
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ntopo_dihedral_template.h
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ntopo_improper_all.cpp
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ntopo_improper_all.h
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ntopo_improper_partial.cpp
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ntopo_improper_partial.h
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ntopo_improper_template.cpp
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ntopo_improper_template.h
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ntopo.cpp
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ntopo.h
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omp_compat.h
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output.cpp
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output.h
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pack.h
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Package.sh
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pair_beck.cpp
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pair_beck.h
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pair_born_coul_dsf.cpp
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pair_born_coul_dsf.h
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pair_born_coul_wolf.cpp
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pair_born_coul_wolf.h
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pair_born.cpp
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pair_born.h
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pair_buck_coul_cut.cpp
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pair_buck_coul_cut.h
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pair_buck.cpp
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pair_buck.h
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pair_coul_cut_global.cpp
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pair_coul_cut_global.h
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pair_coul_cut.cpp
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pair_coul_cut.h
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pair_coul_debye.cpp
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pair_coul_debye.h
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pair_coul_dsf.cpp
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pair_coul_dsf.h
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pair_coul_streitz.cpp
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pair_coul_streitz.h
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pair_coul_wolf.cpp
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pair_coul_wolf.h
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pair_deprecated.cpp
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pair_deprecated.h
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pair_dpd_tstat.cpp
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pair_dpd_tstat.h
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pair_dpd.cpp
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pair_dpd.h
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pair_gauss.cpp
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pair_gauss.h
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pair_hybrid_overlay.cpp
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pair_hybrid_overlay.h
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pair_hybrid_scaled.cpp
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pair_hybrid_scaled.h
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pair_hybrid.cpp
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pair_hybrid.h
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pair_lj96_cut.cpp
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pair_lj96_cut.h
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pair_lj_cubic_const.h
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pair_lj_cubic.cpp
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pair_lj_cubic.h
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pair_lj_cut_coul_cut.cpp
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pair_lj_cut_coul_cut.h
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pair_lj_cut_coul_debye.cpp
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pair_lj_cut_coul_debye.h
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pair_lj_cut_coul_dsf.cpp
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pair_lj_cut_coul_dsf.h
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pair_lj_cut_coul_wolf.cpp
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pair_lj_cut_coul_wolf.h
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pair_lj_cut.cpp
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pair_lj_cut.h
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pair_lj_expand.cpp
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pair_lj_expand.h
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pair_lj_gromacs_coul_gromacs.cpp
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pair_lj_gromacs_coul_gromacs.h
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pair_lj_gromacs.cpp
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pair_lj_gromacs.h
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pair_lj_relres.cpp
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pair_lj_relres.h
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pair_lj_smooth_linear.cpp
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pair_lj_smooth_linear.h
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pair_lj_smooth.cpp
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pair_lj_smooth.h
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pair_mie_cut.cpp
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pair_mie_cut.h
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pair_morse.cpp
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pair_morse.h
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pair_soft.cpp
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pair_soft.h
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pair_table.cpp
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pair_table.h
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pair_ufm.cpp
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pair_ufm.h
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pair_yukawa.cpp
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pair_yukawa.h
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pair_zbl_const.h
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pair_zbl.cpp
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pair_zbl.h
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pair_zero.cpp
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pair_zero.h
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pair.cpp
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pair.h
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pointers.h
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potential_file_reader.cpp
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potential_file_reader.h
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procmap.cpp
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procmap.h
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Purge.list
Merge branch 'master' into prepare-clang-format
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random_mars.cpp
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random_mars.h
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random_park.cpp
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random_park.h
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rcb.cpp
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rcb.h
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read_data.cpp
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read_data.h
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read_dump.cpp
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read_dump.h
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read_restart.cpp
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read_restart.h
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reader_native.cpp
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reader_native.h
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reader_xyz.cpp
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reader_xyz.h
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reader.cpp
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reader.h
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region_block.cpp
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region_block.h
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region_cone.cpp
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region_cone.h
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region_cylinder.cpp
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region_cylinder.h
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region_deprecated.cpp
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region_deprecated.h
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region_intersect.cpp
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region_intersect.h
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region_plane.cpp
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region_plane.h
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region_prism.cpp
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region_prism.h
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region_sphere.cpp
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region_sphere.h
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region_union.cpp
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region_union.h
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region.cpp
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region.h
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replicate.cpp
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replicate.h
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rerun.cpp
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rerun.h
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reset_atom_ids.cpp
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reset_atom_ids.h
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reset_mol_ids.cpp
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reset_mol_ids.h
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respa.cpp
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respa.h
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run.cpp
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run.h
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set.cpp
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set.h
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special.cpp
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special.h
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suffix.h
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table_file_reader.cpp
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table_file_reader.h
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tabular_function.cpp
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tabular_function.h
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text_file_reader.cpp
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text_file_reader.h
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thermo.cpp
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thermo.h
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timer.cpp
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timer.h
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tokenizer.cpp
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tokenizer.h
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universe.cpp
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universe.h
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update.cpp
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update.h
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utils.cpp
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utils.h
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variable.cpp
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variable.h
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velocity.cpp
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velocity.h
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verlet.cpp
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verlet.h
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version.h
step version number for the next patch release
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write_coeff.cpp
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write_coeff.h
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write_data.cpp
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write_data.h
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write_dump.cpp
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write_dump.h
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write_restart.cpp
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write_restart.h
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