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Axel Kohlmeyer 292fc77dce correct broken links to commands
2020-01-30 12:55:59 -05:00
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_ext
update sphinx extension to automatically pad lists to fill tables and avoid errors processing the documentation
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Developer
move developer's guide tex sources back to src/Developer
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Eqs
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JPG
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PDF
Update Colvars library to version 2020-01-27
2020-01-28 14:15:05 -05:00
USER/atc
correct link in AtC html docs
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.gitignore
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angle_charmm.rst
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angle_class2.rst
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angle_coeff.rst
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angle_cosine_buck6d.rst
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angle_cosine_delta.rst
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angle_cosine_periodic.rst
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angle_cosine_shift_exp.rst
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angle_cosine_shift.rst
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angle_cosine_squared.rst
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angle_cosine.rst
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angle_cross.rst
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angle_dipole.rst
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angle_fourier_simple.rst
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angle_fourier.rst
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angle_harmonic.rst
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angle_hybrid.rst
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angle_mm3.rst
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angle_none.rst
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angle_quartic.rst
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angle_sdk.rst
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angle_style.rst
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angle_table.rst
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angle_zero.rst
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angles.rst
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atom_modify.rst
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atom_style.rst
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balance.rst
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bond_class2.rst
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bond_coeff.rst
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bond_fene_expand.rst
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bond_fene.rst
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bond_gromos.rst
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bond_harmonic_shift_cut.rst
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bond_harmonic_shift.rst
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bond_harmonic.rst
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bond_hybrid.rst
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bond_mm3.rst
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bond_morse.rst
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bond_none.rst
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bond_nonlinear.rst
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bond_oxdna.rst
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bond_quartic.rst
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bond_style.rst
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bond_table.rst
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bond_write.rst
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bond_zero.rst
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bonds.rst
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boundary.rst
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box.rst
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Build_basics.rst
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Build_cmake.rst
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Build_development.rst
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Build_extras.rst
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Build_link.rst
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Build_make.rst
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Build_package.rst
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Build_settings.rst
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Build_windows.rst
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Build.rst
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change_box.rst
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clear.rst
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comm_modify.rst
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comm_style.rst
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Commands_all.rst
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Commands_bond.rst
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Commands_category.rst
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Commands_compute.rst
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Commands_fix.rst
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Commands_input.rst
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Commands_kspace.rst
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commands_list.rst
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Commands_pair.rst
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Commands_parse.rst
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Commands_removed.rst
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Commands_structure.rst
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Commands.rst
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compute_ackland_atom.rst
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compute_adf.rst
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compute_angle_local.rst
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compute_angle.rst
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compute_angmom_chunk.rst
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compute_basal_atom.rst
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compute_body_local.rst
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compute_bond_local.rst
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compute_bond.rst
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compute_centro_atom.rst
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compute_chunk_atom.rst
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compute_chunk_spread_atom.rst
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compute_cluster_atom.rst
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compute_cna_atom.rst
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compute_cnp_atom.rst
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compute_com_chunk.rst
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compute_com.rst
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compute_contact_atom.rst
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compute_coord_atom.rst
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compute_damage_atom.rst
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compute_dihedral_local.rst
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compute_dihedral.rst
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compute_dilatation_atom.rst
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compute_dipole_chunk.rst
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compute_displace_atom.rst
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compute_dpd_atom.rst
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compute_dpd.rst
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compute_edpd_temp_atom.rst
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compute_entropy_atom.rst
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compute_erotate_asphere.rst
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compute_erotate_rigid.rst
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compute_erotate_sphere_atom.rst
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compute_erotate_sphere.rst
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compute_event_displace.rst
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compute_fep.rst
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compute_global_atom.rst
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compute_group_group.rst
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compute_gyration_chunk.rst
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compute_gyration_shape_chunk.rst
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compute_gyration_shape.rst
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compute_gyration.rst
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compute_heat_flux.rst
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compute_hexorder_atom.rst
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compute_hma.rst
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compute_improper_local.rst
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compute_improper.rst
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compute_inertia_chunk.rst
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compute_ke_atom_eff.rst
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compute_ke_atom.rst
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compute_ke_eff.rst
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compute_ke_rigid.rst
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compute_ke.rst
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compute_meso_e_atom.rst
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compute_meso_rho_atom.rst
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compute_meso_t_atom.rst
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compute_modify.rst
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compute_momentum.rst
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compute_msd_chunk.rst
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compute_msd_nongauss.rst
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compute_msd.rst
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compute_omega_chunk.rst
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compute_orientorder_atom.rst
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compute_pair_local.rst
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compute_pair.rst
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compute_pe_atom.rst
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compute_pe.rst
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compute_plasticity_atom.rst
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compute_pressure_cylinder.rst
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compute_pressure_uef.rst
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compute_pressure.rst
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compute_property_atom.rst
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compute_property_chunk.rst
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compute_property_local.rst
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compute_ptm_atom.rst
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compute_rdf.rst
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compute_reduce_chunk.rst
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compute_reduce.rst
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compute_rigid_local.rst
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compute_saed.rst
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compute_slice.rst
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compute_smd_contact_radius.rst
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compute_smd_damage.rst
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compute_smd_hourglass_error.rst
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compute_smd_internal_energy.rst
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compute_smd_plastic_strain_rate.rst
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compute_smd_plastic_strain.rst
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compute_smd_rho.rst
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compute_smd_tlsph_defgrad.rst
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compute_smd_tlsph_dt.rst
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compute_smd_tlsph_num_neighs.rst
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compute_smd_tlsph_shape.rst
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compute_smd_tlsph_strain_rate.rst
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compute_smd_tlsph_strain.rst
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compute_smd_tlsph_stress.rst
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compute_smd_triangle_vertices.rst
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compute_smd_ulsph_num_neighs.rst
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compute_smd_ulsph_strain_rate.rst
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compute_smd_ulsph_strain.rst
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compute_smd_ulsph_stress.rst
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compute_smd_vol.rst
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compute_sna_atom.rst
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compute_spin.rst
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compute_stress_atom.rst
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compute_stress_mop.rst
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compute_tally.rst
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compute_tdpd_cc_atom.rst
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compute_temp_asphere.rst
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compute_temp_body.rst
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compute_temp_chunk.rst
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compute_temp_com.rst
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compute_temp_cs.rst
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compute_temp_deform_eff.rst
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compute_temp_deform.rst
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compute_temp_drude.rst
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compute_temp_eff.rst
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compute_temp_partial.rst
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compute_temp_profile.rst
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compute_temp_ramp.rst
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compute_temp_region_eff.rst
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compute_temp_region.rst
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compute_temp_rotate.rst
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compute_temp_sphere.rst
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compute_temp_uef.rst
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compute_temp.rst
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compute_ti.rst
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compute_torque_chunk.rst
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compute_vacf.rst
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compute_vcm_chunk.rst
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compute_voronoi_atom.rst
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compute_xrd.rst
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compute.rst
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computes.rst
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create_atoms.rst
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create_bonds.rst
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create_box.rst
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delete_atoms.rst
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delete_bonds.rst
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dielectric.rst
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dihedral_charmm.rst
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dihedral_class2.rst
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dihedral_coeff.rst
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dihedral_cosine_shift_exp.rst
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dihedral_fourier.rst
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dihedral_harmonic.rst
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dihedral_helix.rst
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dihedral_hybrid.rst
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dihedral_multi_harmonic.rst
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dihedral_nharmonic.rst
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dihedral_none.rst
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dihedral_opls.rst
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dihedral_quadratic.rst
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dihedral_spherical.rst
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dihedral_style.rst
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dihedral_table_cut.rst
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dihedral_table.rst
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dihedral_zero.rst
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dihedrals.rst
merged in current master
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dimension.rst
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displace_atoms.rst
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dump_adios.rst
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dump_cfg_uef.rst
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dump_h5md.rst
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dump_image.rst
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dump_modify.rst
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dump_molfile.rst
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dump_netcdf.rst
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dump_vtk.rst
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dump.rst
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dynamical_matrix.rst
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echo.rst
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Errors_bugs.rst
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Errors_common.rst
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Errors_messages.rst
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Errors_warnings.rst
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Errors.rst
merged in current master
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Examples.rst
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fix_adapt_fep.rst
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fix_adapt.rst
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fix_addforce.rst
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fix_addtorque.rst
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fix_append_atoms.rst
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fix_atc.rst
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fix_atom_swap.rst
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fix_ave_atom.rst
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fix_ave_chunk.rst
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fix_ave_correlate_long.rst
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fix_ave_correlate.rst
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fix_ave_histo.rst
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fix_ave_time.rst
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fix_aveforce.rst
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fix_balance.rst
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fix_bocs.rst
merged in current master
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fix_bond_break.rst
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fix_bond_create.rst
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fix_bond_react.rst
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fix_bond_swap.rst
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fix_box_relax.rst
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fix_client_md.rst
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fix_cmap.rst
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fix_colvars.rst
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fix_controller.rst
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fix_deform.rst
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fix_deposit.rst
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fix_dpd_energy.rst
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fix_dpd_source.rst
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fix_drag.rst
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fix_drude_transform.rst
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fix_drude.rst
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fix_dt_reset.rst
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fix_efield.rst
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fix_ehex.rst
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fix_electron_stopping.rst
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fix_enforce2d.rst
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fix_eos_cv.rst
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fix_eos_table_rx.rst
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fix_eos_table.rst
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fix_evaporate.rst
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fix_external.rst
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fix_ffl.rst
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fix_filter_corotate.rst
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fix_flow_gauss.rst
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fix_freeze.rst
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fix_gcmc.rst
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fix_gld.rst
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fix_gle.rst
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fix_gravity.rst
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fix_grem.rst
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fix_halt.rst
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fix_heat.rst
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fix_hyper_global.rst
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fix_hyper_local.rst
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fix_imd.rst
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fix_indent.rst
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fix_ipi.rst
merged in current master
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fix_langevin_drude.rst
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fix_langevin_eff.rst
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fix_langevin_spin.rst
merged in current master
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fix_langevin.rst
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fix_latte.rst
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fix_lb_fluid.rst
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fix_lb_momentum.rst
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fix_lb_pc.rst
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fix_lb_rigid_pc_sphere.rst
merged in current master
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fix_lb_viscous.rst
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fix_lineforce.rst
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fix_manifoldforce.rst
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fix_meso_move.rst
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fix_meso_stationary.rst
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fix_meso.rst
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fix_modify.rst
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fix_momentum.rst
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fix_move.rst
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fix_mscg.rst
merged in current master
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fix_msst.rst
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fix_mvv_dpd.rst
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fix_neb_spin.rst
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fix_neb.rst
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fix_nh_eff.rst
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fix_nh_uef.rst
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fix_nh.rst
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fix_nph_asphere.rst
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fix_nph_body.rst
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fix_nph_sphere.rst
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fix_nphug.rst
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fix_npt_asphere.rst
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fix_npt_body.rst
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fix_npt_cauchy.rst
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fix_npt_sphere.rst
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fix_nve_asphere_noforce.rst
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fix_nve_asphere.rst
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fix_nve_awpmd.rst
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fix_nve_body.rst
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fix_nve_dot.rst
merged in current master
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fix_nve_dotc_langevin.rst
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fix_nve_eff.rst
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fix_nve_limit.rst
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fix_nve_line.rst
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fix_nve_manifold_rattle.rst
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fix_nve_noforce.rst
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fix_nve_sphere.rst
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fix_nve_spin.rst
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fix_nve_tri.rst
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fix_nve.rst
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fix_nvk.rst
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fix_nvt_asphere.rst
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fix_nvt_body.rst
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fix_nvt_manifold_rattle.rst
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fix_nvt_sllod_eff.rst
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fix_nvt_sllod.rst
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fix_nvt_sphere.rst
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fix_oneway.rst
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fix_orient.rst
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fix_phonon.rst
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fix_pimd.rst
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fix_planeforce.rst
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fix_plumed.rst
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fix_poems.rst
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fix_pour.rst
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fix_precession_spin.rst
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fix_press_berendsen.rst
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fix_print.rst
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fix_propel_self.rst
change mode of propel/self to quat instead of quaternion
2020-01-20 17:41:20 +01:00
fix_property_atom.rst
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2020-01-23 16:52:38 -05:00
fix_python_invoke.rst
merged in current master
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fix_python_move.rst
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fix_qbmsst.rst
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fix_qeq_comb.rst
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fix_qeq_reax.rst
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fix_qeq.rst
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fix_qmmm.rst
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fix_qtb.rst
merged in current master
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fix_reaxc_bonds.rst
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fix_reaxc_species.rst
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fix_recenter.rst
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fix_restrain.rst
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fix_rhok.rst
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fix_rigid_meso.rst
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fix_rigid.rst
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fix_rx.rst
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fix_saed_vtk.rst
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fix_setforce.rst
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fix_shake.rst
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fix_shardlow.rst
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fix_smd_adjust_dt.rst
merged in current master
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fix_smd_integrate_tlsph.rst
merged in current master
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fix_smd_integrate_ulsph.rst
merged in current master
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fix_smd_move_triangulated_surface.rst
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fix_smd_setvel.rst
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fix_smd_wall_surface.rst
merged in current master
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fix_smd.rst
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fix_spring_chunk.rst
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fix_spring_rg.rst
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fix_spring_self.rst
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fix_spring.rst
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fix_srd.rst
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fix_store_force.rst
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fix_store_state.rst
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fix_temp_berendsen.rst
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fix_temp_csvr.rst
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fix_temp_rescale_eff.rst
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fix_temp_rescale.rst
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fix_tfmc.rst
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fix_thermal_conductivity.rst
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fix_ti_spring.rst
merged in current master
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fix_tmd.rst
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fix_ttm.rst
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fix_tune_kspace.rst
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fix_vector.rst
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fix_viscosity.rst
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fix_viscous.rst
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fix_wall_body_polygon.rst
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fix_wall_body_polyhedron.rst
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fix_wall_ees.rst
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fix_wall_gran_region.rst
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fix_wall_gran.rst
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fix_wall_piston.rst
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fix_wall_reflect_stochastic.rst
add rst version of doc file
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fix_wall_reflect.rst
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fix_wall_region.rst
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fix_wall_srd.rst
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fix_wall.rst
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2020-01-23 16:52:38 -05:00
fix.rst
documentation and examples cleanup for fix propel/self
2020-01-19 13:29:52 -05:00
fixes.rst
merged in current master
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group2ndx.rst
merged in current master
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group.rst
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Howto_2d.rst
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Howto_barostat.rst
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Howto_bash.rst
repair incorrect conversions on [*] expressions by txt2rst
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Howto_bioFF.rst
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Howto_body.rst
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Howto_chunk.rst
merged in current master
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Howto_client_server.rst
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Howto_coreshell.rst
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Howto_kappa.rst
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Howto_library.rst
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Howto_manifold.rst
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Howto_multiple.rst
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Howto_nemd.rst
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Howto_polarizable.rst
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Howto_replica.rst
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Howto_spc.rst
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Howto_spherical.rst
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Howto_spins.rst
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Howto_tip3p.rst
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Howto_triclinic.rst
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Howto_viscosity.rst
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Howto_walls.rst
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Howto.rst
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hyper.rst
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if.rst
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improper_class2.rst
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improper_coeff.rst
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improper_cvff.rst
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improper_distance.rst
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improper_fourier.rst
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improper_harmonic.rst
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improper_hybrid.rst
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improper_inversion_harmonic.rst
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improper_none.rst
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improper_ring.rst
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improper_sqdistharm.rst
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improper_style.rst
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improper_umbrella.rst
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improper_zero.rst
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impropers.rst
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include.rst
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info.rst
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Install_conda.rst
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Install_git.rst
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Install_linux.rst
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Install_mac.rst
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Install_patch.rst
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Install_svn.rst
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Install_tarball.rst
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Install_windows.rst
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Install.rst
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Intro_authors.rst
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Intro_features.rst
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Intro_website.rst
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Intro.rst
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jump.rst
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kim_commands.rst
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kspace_modify.rst
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kspace_style.rst
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label.rst
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lattice.rst
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log.rst
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mass.rst
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message.rst
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min_modify.rst
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min_spin.rst
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min_style.rst
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minimize.rst
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molecule.rst
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neb_spin.rst
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neb.rst
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neigh_modify.rst
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neighbor.rst
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newton.rst
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next.rst
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package.rst
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Packages_details.rst
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Packages_standard.rst
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Packages_user.rst
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Packages.rst
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pair_adp.rst
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pair_agni.rst
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pair_airebo.rst
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pair_atm.rst
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pair_awpmd.rst
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pair_beck.rst
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pair_body_nparticle.rst
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pair_body_rounded_polygon.rst
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pair_body_rounded_polyhedron.rst
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pair_bop.rst
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pair_born.rst
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pair_brownian.rst
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pair_buck6d_coul_gauss.rst
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pair_buck_long.rst
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pair_buck.rst
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pair_charmm.rst
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pair_class2.rst
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pair_coeff.rst
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pair_colloid.rst
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pair_comb.rst
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pair_cosine_squared.rst
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pair_coul_diel.rst
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pair_coul_shield.rst
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pair_coul.rst
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pair_cs.rst
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pair_dipole.rst
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pair_dpd_fdt.rst
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pair_dpd.rst
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pair_drip.rst
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pair_dsmc.rst
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pair_e3b.rst
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pair_eam.rst
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pair_edip.rst
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pair_eff.rst
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pair_eim.rst
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pair_exp6_rx.rst
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pair_extep.rst
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pair_fep_soft.rst
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pair_gauss.rst
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pair_gayberne.rst
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pair_gran.rst
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pair_granular.rst
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pair_gromacs.rst
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pair_gw.rst
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pair_hbond_dreiding.rst
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pair_hybrid.rst
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pair_ilp_graphene_hbn.rst
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pair_kim.rst
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pair_kolmogorov_crespi_full.rst
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pair_kolmogorov_crespi_z.rst
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pair_lcbop.rst
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pair_lebedeva_z.rst
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pair_line_lj.rst
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pair_list.rst
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pair_lj96.rst
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pair_lj_cubic.rst
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pair_lj_expand.rst
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pair_lj_long.rst
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pair_lj_smooth_linear.rst
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pair_lj_smooth.rst
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pair_lj_switch3_coulgauss_long.rst
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pair_lj.rst
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pair_local_density.rst
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pair_lubricate.rst
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pair_lubricateU.rst
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pair_mdf.rst
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pair_meam_spline.rst
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pair_meam_sw_spline.rst
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pair_meamc.rst
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pair_meso.rst
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pair_mesocnt.rst
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pair_mgpt.rst
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pair_mie.rst
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pair_mm3_switch3_coulgauss_long.rst
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pair_modify.rst
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pair_momb.rst
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pair_morse.rst
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pair_multi_lucy_rx.rst
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pair_multi_lucy.rst
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pair_nb3b_harmonic.rst
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pair_nm.rst
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pair_none.rst
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pair_oxdna2.rst
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pair_oxdna.rst
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pair_oxrna2.rst
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pair_peri.rst
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pair_polymorphic.rst
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pair_python.rst
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pair_quip.rst
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pair_reaxc.rst
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pair_resquared.rst
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pair_sdk.rst
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pair_sdpd_taitwater_isothermal.rst
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pair_smd_hertz.rst
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pair_smd_tlsph.rst
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pair_smd_ulsph.rst
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pair_smtbq.rst
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pair_snap.rst
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pair_soft.rst
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pair_sph_heatconduction.rst
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pair_sph_idealgas.rst
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pair_sph_lj.rst
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pair_sph_rhosum.rst
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pair_sph_taitwater_morris.rst
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pair_sph_taitwater.rst
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pair_spin_dipole.rst
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pair_spin_dmi.rst
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pair_spin_exchange.rst
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pair_spin_magelec.rst
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pair_spin_neel.rst
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pair_srp.rst
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pair_style.rst
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pair_sw.rst
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pair_table_rx.rst
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pair_table.rst
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pair_tersoff_mod.rst
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pair_tersoff_zbl.rst
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pair_tersoff.rst
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pair_thole.rst
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pair_tri_lj.rst
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pair_ufm.rst
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pair_vashishta.rst
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pair_write.rst
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pair_yukawa_colloid.rst
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pair_yukawa.rst
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pair_zbl.rst
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pair_zero.rst
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pairs.rst
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partition.rst
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prd.rst
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print.rst
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processors.rst
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Python_call.rst
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Python_examples.rst
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Python_head.rst
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Python_install.rst
expand explanations about setting the python version for the python wrapper
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Python_library.rst
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Python_mpi.rst
add mpi4py url and expand/update the python with MPI introduction
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Python_overview.rst
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Python_pylammps.rst
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Python_run.rst
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Python_shlib.rst
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Python_test.rst
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python.rst
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quit.rst
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read_data.rst
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read_dump.rst
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read_restart.rst
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region.rst
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replicate.rst
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rerun.rst
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reset_ids.rst
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reset_timestep.rst
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restart.rst
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Run_basics.rst
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Run_head.rst
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Run_options.rst
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Run_output.rst
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run_style.rst
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Run_windows.rst
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run.rst
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server_mc.rst
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server_md.rst
merged in current master
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server.rst
convert documentation to rst format and remove corresponding txt files
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set.rst
correct broken links to commands
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shell.rst
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special_bonds.rst
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Speed_bench.rst
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Speed_compare.rst
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Speed_gpu.rst
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Speed_intel.rst
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Speed_kokkos.rst
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Speed_measure.rst
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Speed_omp.rst
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Speed_opt.rst
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Speed_packages.rst
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Speed_tips.rst
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Speed.rst
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suffix.rst
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tad.rst
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temper_grem.rst
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temper_npt.rst
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temper.rst
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thermo_modify.rst
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thermo_style.rst
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thermo.rst
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third_order.rst
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timer.rst
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timestep.rst
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Tools.rst
correct malformed tables
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uncompute.rst
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undump.rst
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unfix.rst
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units.rst
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variable.rst
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velocity.rst
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write_coeff.rst
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write_data.rst
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write_dump.rst
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write_restart.rst
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