Loading doc/src/angles.rst +2 −22 Original line number Diff line number Diff line Loading @@ -4,26 +4,6 @@ Angle Styles .. toctree:: :maxdepth: 1 :glob: angle_charmm angle_class2 angle_cosine angle_cosine_buck6d angle_cosine_delta angle_cosine_periodic angle_cosine_shift angle_cosine_shift_exp angle_cosine_squared angle_cross angle_dipole angle_fourier angle_fourier_simple angle_harmonic angle_hybrid angle_mm3 angle_none angle_quartic angle_sdk angle_table angle_zero angle_* doc/src/bonds.rst +2 −17 Original line number Diff line number Diff line Loading @@ -4,21 +4,6 @@ Bond Styles .. toctree:: :maxdepth: 1 :glob: bond_class2 bond_fene bond_fene_expand bond_gromos bond_harmonic bond_harmonic_shift bond_harmonic_shift_cut bond_hybrid bond_mm3 bond_morse bond_none bond_nonlinear bond_oxdna bond_quartic bond_table bond_zero bond_* doc/src/computes.rst +2 −129 Original line number Diff line number Diff line Loading @@ -4,133 +4,6 @@ Computes .. toctree:: :maxdepth: 1 :glob: compute_ackland_atom compute_adf compute_angle compute_angle_local compute_angmom_chunk compute_basal_atom compute_body_local compute_bond compute_bond_local compute_centro_atom compute_chunk_atom compute_chunk_spread_atom compute_cluster_atom compute_cna_atom compute_cnp_atom compute_com compute_com_chunk compute_contact_atom compute_coord_atom compute_damage_atom compute_dihedral compute_dihedral_local compute_dilatation_atom compute_dipole_chunk compute_displace_atom compute_dpd compute_dpd_atom compute_edpd_temp_atom compute_entropy_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere compute_erotate_sphere_atom compute_event_displace compute_fep compute_global_atom compute_group_group compute_gyration compute_gyration_chunk compute_gyration_shape compute_heat_flux compute_hexorder_atom compute_hma compute_improper compute_improper_local compute_inertia_chunk compute_ke compute_ke_atom compute_ke_atom_eff compute_ke_eff compute_ke_rigid compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom compute_momentum compute_msd compute_msd_chunk compute_msd_nongauss compute_omega_chunk compute_orientorder_atom compute_pair compute_pair_local compute_pe compute_pe_atom compute_plasticity_atom compute_pressure compute_pressure_cylinder compute_pressure_uef compute_property_atom compute_property_chunk compute_property_local compute_ptm_atom compute_rdf compute_reduce compute_reduce_chunk compute_rigid_local compute_saed compute_slice compute_smd_contact_radius compute_smd_damage compute_smd_hourglass_error compute_smd_internal_energy compute_smd_plastic_strain compute_smd_plastic_strain_rate compute_smd_rho compute_smd_tlsph_defgrad compute_smd_tlsph_dt compute_smd_tlsph_num_neighs compute_smd_tlsph_shape compute_smd_tlsph_strain compute_smd_tlsph_strain_rate compute_smd_tlsph_stress compute_smd_triangle_vertices compute_smd_ulsph_num_neighs compute_smd_ulsph_strain compute_smd_ulsph_strain_rate compute_smd_ulsph_stress compute_smd_vol compute_sna_atom compute_spin compute_stress_atom compute_stress_mop compute_tally compute_tdpd_cc_atom compute_temp compute_temp_asphere compute_temp_body compute_temp_chunk compute_temp_com compute_temp_cs compute_temp_deform compute_temp_deform_eff compute_temp_drude compute_temp_eff compute_temp_partial compute_temp_profile compute_temp_ramp compute_temp_region compute_temp_region_eff compute_temp_rotate compute_temp_sphere compute_temp_uef compute_ti compute_torque_chunk compute_vacf compute_vcm_chunk compute_voronoi_atom compute_xrd compute_* doc/src/dihedrals.rst +2 −32 Original line number Diff line number Diff line Loading @@ -4,36 +4,6 @@ Dihedral Styles .. toctree:: :maxdepth: 1 :glob: dihedral_charmm dihedral_class2 dihedral_cosine_shift_exp dihedral_fourier dihedral_harmonic dihedral_helix dihedral_hybrid dihedral_multi_harmonic dihedral_nharmonic dihedral_none dihedral_opls dihedral_quadratic dihedral_spherical dihedral_table dihedral_table_cut dihedral_zero dihedral_charmm dihedral_class2 dihedral_cosine_shift_exp dihedral_fourier dihedral_harmonic dihedral_helix dihedral_hybrid dihedral_multi_harmonic dihedral_nharmonic dihedral_none dihedral_opls dihedral_quadratic dihedral_spherical dihedral_table dihedral_zero dihedral_* doc/src/fixes.rst +2 −182 Original line number Diff line number Diff line Loading @@ -4,186 +4,6 @@ Fixes .. toctree:: :maxdepth: 1 :glob: fix_adapt fix_adapt_fep fix_addforce fix_addtorque fix_append_atoms fix_atc fix_atom_swap fix_ave_atom fix_ave_chunk fix_ave_correlate fix_ave_correlate_long fix_ave_histo fix_ave_time fix_aveforce fix_balance fix_bocs fix_bond_break fix_bond_create fix_bond_swap fix_bond_react fix_box_relax fix_client_md fix_cmap fix_colvars fix_controller fix_deform fix_deposit fix_drag fix_drude fix_drude_transform fix_dpd_energy fix_dpd_source fix_dt_reset fix_efield fix_ehex fix_electron_stopping fix_enforce2d fix_eos_cv fix_eos_table fix_eos_table_rx fix_evaporate fix_external fix_ffl fix_filter_corotate fix_flow_gauss fix_freeze fix_gcmc fix_gld fix_gle fix_gravity fix_grem fix_halt fix_heat fix_hyper_global fix_hyper_local fix_imd fix_indent fix_ipi fix_langevin fix_langevin_drude fix_langevin_eff fix_langevin_spin fix_latte fix_lb_fluid fix_lb_momentum fix_lb_pc fix_lb_rigid_pc_sphere fix_lb_viscous fix_lineforce fix_manifoldforce fix_meso fix_meso_move fix_meso_stationary fix_momentum fix_move fix_mscg fix_msst fix_mvv_dpd fix_neb fix_neb_spin fix_nh fix_nh_eff fix_nh_uef fix_nph_asphere fix_nph_body fix_nph_sphere fix_nphug fix_npt_asphere fix_npt_body fix_npt_sphere fix_nve fix_nve_asphere fix_nve_asphere_noforce fix_nve_awpmd fix_nve_body fix_nve_dot fix_nve_dotc_langevin fix_nve_eff fix_nve_limit fix_nve_line fix_nve_manifold_rattle fix_nve_noforce fix_nve_sphere fix_nve_spin fix_nve_tri fix_nvk fix_nvt_asphere fix_nvt_body fix_nvt_manifold_rattle fix_nvt_sllod fix_nvt_sllod_eff fix_nvt_sphere fix_oneway fix_orient fix_phonon fix_pimd fix_planeforce fix_plumed fix_poems fix_pour fix_precession_spin fix_press_berendsen fix_print fix_property_atom fix_python_invoke fix_python_move fix_qbmsst fix_qeq fix_qeq_comb fix_qeq_reax fix_qmmm fix_qtb fix_reaxc_bonds fix_reaxc_species fix_recenter fix_restrain fix_rhok fix_rigid fix_rigid_meso fix_rx fix_saed_vtk fix_setforce fix_shake fix_shardlow fix_smd fix_smd_adjust_dt fix_smd_integrate_tlsph fix_smd_integrate_ulsph fix_smd_move_triangulated_surface fix_smd_setvel fix_smd_wall_surface fix_spring fix_spring_chunk fix_spring_rg fix_spring_self fix_srd fix_store_force fix_store_state fix_temp_berendsen fix_temp_csvr fix_temp_rescale fix_temp_rescale_eff fix_tfmc fix_thermal_conductivity fix_ti_spring fix_tmd fix_ttm fix_tune_kspace fix_vector fix_viscosity fix_viscous fix_wall fix_wall_body_polygon fix_wall_body_polyhedron fix_wall_ees fix_wall_gran fix_wall_gran_region fix_wall_piston fix_wall_reflect fix_wall_region fix_wall_srd fix_* Loading
doc/src/angles.rst +2 −22 Original line number Diff line number Diff line Loading @@ -4,26 +4,6 @@ Angle Styles .. toctree:: :maxdepth: 1 :glob: angle_charmm angle_class2 angle_cosine angle_cosine_buck6d angle_cosine_delta angle_cosine_periodic angle_cosine_shift angle_cosine_shift_exp angle_cosine_squared angle_cross angle_dipole angle_fourier angle_fourier_simple angle_harmonic angle_hybrid angle_mm3 angle_none angle_quartic angle_sdk angle_table angle_zero angle_*
doc/src/bonds.rst +2 −17 Original line number Diff line number Diff line Loading @@ -4,21 +4,6 @@ Bond Styles .. toctree:: :maxdepth: 1 :glob: bond_class2 bond_fene bond_fene_expand bond_gromos bond_harmonic bond_harmonic_shift bond_harmonic_shift_cut bond_hybrid bond_mm3 bond_morse bond_none bond_nonlinear bond_oxdna bond_quartic bond_table bond_zero bond_*
doc/src/computes.rst +2 −129 Original line number Diff line number Diff line Loading @@ -4,133 +4,6 @@ Computes .. toctree:: :maxdepth: 1 :glob: compute_ackland_atom compute_adf compute_angle compute_angle_local compute_angmom_chunk compute_basal_atom compute_body_local compute_bond compute_bond_local compute_centro_atom compute_chunk_atom compute_chunk_spread_atom compute_cluster_atom compute_cna_atom compute_cnp_atom compute_com compute_com_chunk compute_contact_atom compute_coord_atom compute_damage_atom compute_dihedral compute_dihedral_local compute_dilatation_atom compute_dipole_chunk compute_displace_atom compute_dpd compute_dpd_atom compute_edpd_temp_atom compute_entropy_atom compute_erotate_asphere compute_erotate_rigid compute_erotate_sphere compute_erotate_sphere_atom compute_event_displace compute_fep compute_global_atom compute_group_group compute_gyration compute_gyration_chunk compute_gyration_shape compute_heat_flux compute_hexorder_atom compute_hma compute_improper compute_improper_local compute_inertia_chunk compute_ke compute_ke_atom compute_ke_atom_eff compute_ke_eff compute_ke_rigid compute_meso_e_atom compute_meso_rho_atom compute_meso_t_atom compute_momentum compute_msd compute_msd_chunk compute_msd_nongauss compute_omega_chunk compute_orientorder_atom compute_pair compute_pair_local compute_pe compute_pe_atom compute_plasticity_atom compute_pressure compute_pressure_cylinder compute_pressure_uef compute_property_atom compute_property_chunk compute_property_local compute_ptm_atom compute_rdf compute_reduce compute_reduce_chunk compute_rigid_local compute_saed compute_slice compute_smd_contact_radius compute_smd_damage compute_smd_hourglass_error compute_smd_internal_energy compute_smd_plastic_strain compute_smd_plastic_strain_rate compute_smd_rho compute_smd_tlsph_defgrad compute_smd_tlsph_dt compute_smd_tlsph_num_neighs compute_smd_tlsph_shape compute_smd_tlsph_strain compute_smd_tlsph_strain_rate compute_smd_tlsph_stress compute_smd_triangle_vertices compute_smd_ulsph_num_neighs compute_smd_ulsph_strain compute_smd_ulsph_strain_rate compute_smd_ulsph_stress compute_smd_vol compute_sna_atom compute_spin compute_stress_atom compute_stress_mop compute_tally compute_tdpd_cc_atom compute_temp compute_temp_asphere compute_temp_body compute_temp_chunk compute_temp_com compute_temp_cs compute_temp_deform compute_temp_deform_eff compute_temp_drude compute_temp_eff compute_temp_partial compute_temp_profile compute_temp_ramp compute_temp_region compute_temp_region_eff compute_temp_rotate compute_temp_sphere compute_temp_uef compute_ti compute_torque_chunk compute_vacf compute_vcm_chunk compute_voronoi_atom compute_xrd compute_*
doc/src/dihedrals.rst +2 −32 Original line number Diff line number Diff line Loading @@ -4,36 +4,6 @@ Dihedral Styles .. toctree:: :maxdepth: 1 :glob: dihedral_charmm dihedral_class2 dihedral_cosine_shift_exp dihedral_fourier dihedral_harmonic dihedral_helix dihedral_hybrid dihedral_multi_harmonic dihedral_nharmonic dihedral_none dihedral_opls dihedral_quadratic dihedral_spherical dihedral_table dihedral_table_cut dihedral_zero dihedral_charmm dihedral_class2 dihedral_cosine_shift_exp dihedral_fourier dihedral_harmonic dihedral_helix dihedral_hybrid dihedral_multi_harmonic dihedral_nharmonic dihedral_none dihedral_opls dihedral_quadratic dihedral_spherical dihedral_table dihedral_zero dihedral_*
doc/src/fixes.rst +2 −182 Original line number Diff line number Diff line Loading @@ -4,186 +4,6 @@ Fixes .. toctree:: :maxdepth: 1 :glob: fix_adapt fix_adapt_fep fix_addforce fix_addtorque fix_append_atoms fix_atc fix_atom_swap fix_ave_atom fix_ave_chunk fix_ave_correlate fix_ave_correlate_long fix_ave_histo fix_ave_time fix_aveforce fix_balance fix_bocs fix_bond_break fix_bond_create fix_bond_swap fix_bond_react fix_box_relax fix_client_md fix_cmap fix_colvars fix_controller fix_deform fix_deposit fix_drag fix_drude fix_drude_transform fix_dpd_energy fix_dpd_source fix_dt_reset fix_efield fix_ehex fix_electron_stopping fix_enforce2d fix_eos_cv fix_eos_table fix_eos_table_rx fix_evaporate fix_external fix_ffl fix_filter_corotate fix_flow_gauss fix_freeze fix_gcmc fix_gld fix_gle fix_gravity fix_grem fix_halt fix_heat fix_hyper_global fix_hyper_local fix_imd fix_indent fix_ipi fix_langevin fix_langevin_drude fix_langevin_eff fix_langevin_spin fix_latte fix_lb_fluid fix_lb_momentum fix_lb_pc fix_lb_rigid_pc_sphere fix_lb_viscous fix_lineforce fix_manifoldforce fix_meso fix_meso_move fix_meso_stationary fix_momentum fix_move fix_mscg fix_msst fix_mvv_dpd fix_neb fix_neb_spin fix_nh fix_nh_eff fix_nh_uef fix_nph_asphere fix_nph_body fix_nph_sphere fix_nphug fix_npt_asphere fix_npt_body fix_npt_sphere fix_nve fix_nve_asphere fix_nve_asphere_noforce fix_nve_awpmd fix_nve_body fix_nve_dot fix_nve_dotc_langevin fix_nve_eff fix_nve_limit fix_nve_line fix_nve_manifold_rattle fix_nve_noforce fix_nve_sphere fix_nve_spin fix_nve_tri fix_nvk fix_nvt_asphere fix_nvt_body fix_nvt_manifold_rattle fix_nvt_sllod fix_nvt_sllod_eff fix_nvt_sphere fix_oneway fix_orient fix_phonon fix_pimd fix_planeforce fix_plumed fix_poems fix_pour fix_precession_spin fix_press_berendsen fix_print fix_property_atom fix_python_invoke fix_python_move fix_qbmsst fix_qeq fix_qeq_comb fix_qeq_reax fix_qmmm fix_qtb fix_reaxc_bonds fix_reaxc_species fix_recenter fix_restrain fix_rhok fix_rigid fix_rigid_meso fix_rx fix_saed_vtk fix_setforce fix_shake fix_shardlow fix_smd fix_smd_adjust_dt fix_smd_integrate_tlsph fix_smd_integrate_ulsph fix_smd_move_triangulated_surface fix_smd_setvel fix_smd_wall_surface fix_spring fix_spring_chunk fix_spring_rg fix_spring_self fix_srd fix_store_force fix_store_state fix_temp_berendsen fix_temp_csvr fix_temp_rescale fix_temp_rescale_eff fix_tfmc fix_thermal_conductivity fix_ti_spring fix_tmd fix_ttm fix_tune_kspace fix_vector fix_viscosity fix_viscous fix_wall fix_wall_body_polygon fix_wall_body_polyhedron fix_wall_ees fix_wall_gran fix_wall_gran_region fix_wall_piston fix_wall_reflect fix_wall_region fix_wall_srd fix_*
