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Definition at line 12 of file nr_jacobi.C.
Referenced by SaveTrajectoryFltkMenu::act_on_command, MoleculeList::activate, Scene::activate_adv_light, Scene::activate_light, MoleculeList::active, BaseMolecule::add_angle, MoleculeGraphics::add_cone, MoleculeGraphics::add_cylinder, BaseMolecule::add_dihedral, colvarvalue::add_elem, BaseMolecule::add_improper, MoleculeList::add_rep, MoleculeGraphics::add_sphere, Tool::addplaneconstraint, Scene::adv_light_active, Scene::adv_light_attenuation, Scene::adv_light_color, Scene::adv_light_color_default, Scene::adv_light_get_attenuation, Scene::adv_light_get_spotlight, Scene::adv_light_pos, Scene::adv_light_pos_default, Scene::adv_light_spotlight, analyze_selection_aligned, analyze_selection_aligned_dispatch, anterpolation, BaseMolecule::atom, DrawMolItem::atom_displayed, DrawMolecule::atom_displayed, BaseMolecule::atom_fragment, BaseMolecule::atom_residue, atomsel_AsAtomSel, colvar_grid_gradient::average, basis_change, bin_evaluation, binomial, DisplayDevice::cache_name, CUDAQuickSurf::calc_surf, GeometryMol::calculate_all, MoleculeList::center_all_molecules, cephesfastexpf, MoleculeList::change_rep, DrawMolecule::change_rep, MoleculeList::change_repcolor, MoleculeList::change_repmat, MoleculeList::change_repmethod, MoleculeList::change_repsel, Animation::check_event, JString::chop, clip_ray_by_plane, CmdAnimWriteFile::CmdAnimWriteFile, CmdLabelAdd::CmdLabelAdd, CmdLabelDelete::CmdLabelDelete, CmdLabelShow::CmdLabelShow, CmdLabelTextFormat::CmdLabelTextFormat, CmdLabelTextOffset::CmdLabelTextOffset, CmdMolNumPeriodic::CmdMolNumPeriodic, VMDApp::color_category, VMDApp::color_category_item, Scene::color_default_value, VMDApp::color_name, Scene::color_name, Scene::color_value, VMDApp::colorscale_method_menuname, Scene::colorscale_method_menuname, VMDApp::colorscale_method_name, Scene::colorscale_method_name, colvarparse::colvarparse, Combinations::Combinations, combine_arguments, VolMapCreate::combo_addframe, VolMapCreate::combo_export, RadianceDisplayDevice::comment, DrawMolecule::component, VolMapCreateILS::compute, compute_allatoms, compute_dihed_energy, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, NanoShaperInterface::compute_from_file, MSMSInterface::compute_from_file, MSMSInterface::compute_from_socket, compute_norm2_stats, compute_occupancy_monoatom, compute_occupancy_multiatom, compute_pbcminmax, colvar::selfcoordnum::compute_selfcoordnum, RadianceDisplayDevice::cone_trunc, cuda_find_energy_exclusions, cuda_occupancy_monoatom, cuda_occupancy_multiatom, cuda_occupancy_thread, cuda_shortrange, cuda_shortrange_nonperiodic, RadianceDisplayDevice::cylinder, cylinder_array_color_intersect, cylinder_array_intersect, cylinder_full, Scene::define_adv_light, Scene::define_light, MoleculeList::del_all_molecules, GeometryList::del_geometry, MoleculeList::del_molecule, MoleculeList::del_rep, DrawMolecule::del_rep, DrawMolecule::delete_frame, MoleculeGraphics::delete_id, MaterialList::delete_material, Displayable::delete_material, OSPRay2Renderer::destroy_scene, ANARIRender::destroy_scene, MoleculeList::displayed, FileRenderer::do_activate_adv_light, OpenGLRenderer::do_activate_light, FileRenderer::do_activate_light, FileRenderer::do_define_adv_light, OpenGLRenderer::do_define_light, FileRenderer::do_define_light, doublefac, VolumetricData::downsample, energythread, CommandQueue::execute_all, QMData::expand_atompos, QMData::expand_basis_array, fac, VMDApp::filerender_name, VMDApp::filerender_prettyname, fill_atom_bins, IdList::find, find_distance_exclusions, find_energy_exclusions, find_first_selection_aligned, find_last_selection_aligned, find_minmax, find_minmax_all, find_minmax_selected, find_within_routine, MoleculeList::fix, MoleculeList::fixed, BaseMolecule::fragment, generateTriangleColorNormal, generateTriangleNormals, geom2dict, GeometryList::geom_list, GeometryList::geom_list_name, GeometryMol::GeometryMol, Symmetry::get_axisorder, AtomRep::get_data, DrawMolecule::get_frame, Symmetry::get_pointgroup, Symmetry::get_rotreflectorder, DispCmdTriMesh::getpointers, GeometryList::getTextFormat, GeometryList::getTextOffset, getvalues, glwin_init_exts, glwin_query_extension, glwin_spheremap_draw_tex, glx_query_extension, colvar_grid_scalar::gradient_finite_diff, colvar_grid_count::gradient_finite_diff, TextInterp::graph_label_cb, TclTextInterp::graph_label_cb, GraphLabelEvent::GraphLabelEvent, MoleculeList::hide, hill_reilly_ring_pucker, imd_htonl, imd_ntohl, imd_readn, imd_recv_fcoords, imd_recv_mdcomm, imd_send_fcoords, imd_send_mdcomm, imd_writen, MoleculeList::inactivate, MolAtom::init, BaseMolecule::init_atoms, colvarmodule::integer_power, MoleculeList::is_top, jacobi, keyword_delimiters_right, VMDApp::label_add, VMDApp::label_delete, VMDApp::label_set_textformat, VMDApp::label_set_textoffset, VMDApp::label_show, layout_fr, least_squares, Scene::light_active, Scene::light_color, Scene::light_color_default, VMDApp::light_highlight, VMDApp::light_move, VMDApp::light_on, Scene::light_pos, Scene::light_pos_default, VMDApp::light_rotate, RadianceDisplayDevice::line, linklist_evaluation, linklist_hashing, colvar_grid_count::log_gradient_finite_diff, make_neighborlist, make_neighborlist_sym, MoleculeList::make_top, VMDApp::material_rename, MatrixFitRMS, measure_cluster, measure_fit, measure_pbc_neighbors, minmax_1fv_aligned, minmaxmean_1fv_aligned, MoleculeList::molecule, VMDApp::molrep_set_pbc_images, VMDApp::molrep_set_smoothing, Scene::move_adv_light, Scene::move_light, Msmpot_compute_shortrng_bin_hashing, Msmpot_cuda_setup_shortrng, MyMatrixFitRMS, Scene::nearest_index, FileRenderer::nearest_index, colvarmodule::num_biases_feature, colvarmodule::num_biases_type, colvarmodule::num_variables_feature, VMDDisplayList::operator new, Displayable::operator new, DrawMolecule::override_current_frame, TextInterp::pick_selection_cb, PickSelectionEvent::PickSelectionEvent, RadianceDisplayDevice::point, DispCmdCylinder::putdata, DispCmdTriMesh::putdata, DispCmdPolyLineArray::putdata, DispCmdLineArray::putdata, py_get_vector, py_set_smoothing, py_set_visible, colvar_grid::read_multicol, MolFilePlugin::read_volumetric, SortableArray< DepthSortObject >::remove, ResizeArray< ShapeClass >::remove, Displayable::remove_child, FileRenderer::render, DisplayDevice::render_name, colvarmodule::rotation::request_group1_gradients, colvarmodule::rotation::request_group2_gradients, BaseMolecule::residue, colvarmodule::vector1d::resize, PickModeMoveRep::rotate, PickModeMoveFragment::rotate, PickModeMoveResidue::rotate, Scene::rotate_light, CommandQueue::runcommand, AtomGrid::scramble_array, ToolFltkMenu::select_tool, ToolFltkMenu::select_tool_type, IMDMgr::send_forces, OSPRayRenderer::set_camera_dof_fnumber, OSPRay2Renderer::set_camera_dof_fnumber, OptiXRenderer::set_camera_dof_fnumber, ANARIRender::set_camera_dof_fnumber, RadianceDisplayDevice::set_color, Scene::set_color_value, OpenGLDisplayDevice::set_cursor, FltkOpenGLDisplayDevice::set_cursor, myFl_Chart::set_data, ToolFltkMenu::set_forcescale, Symmetry::set_maxnumatoms, MolFilePlugin::set_natoms, ToolFltkMenu::set_offset, GraphicsFltkMenu::set_pbc, DrawMolItem::set_pbc_images, ToolFltkMenu::set_positionscale, DrawMolItem::set_smoothing, ToolFltkMenu::set_springscale, ToolFltkMenu::set_toolrep, Tool::setplaneconstraint, GeometryList::setTextFormat, GeometryList::setTextOffset, setup_domain, setup_hierarchy, setup_mapinterpcoef_1d, setup_nonperiodic_hlevelparams_1d, setup_periodic_hlevelparams_1d, MoleculeList::show, GeometryList::show_geometry, RadianceDisplayDevice::sphere, RenderManDisplayDevice::square, RadianceDisplayDevice::square, LibGelatoDisplayDevice::square, GelatoDisplayDevice::square, DisplayDevice::stereo_name, stripslashes, strupcmp, strupncmp, colvarproxy_tcl::tcl_run_colvar_gradient_callback, tea, text_cmd_label, text_cmd_light, text_cmd_point_light, text_cmd_render, tighten_bin_neighborhood, Timestep::Timestep, TclTextInterp::timestep_cb, TrajectoryReadEvent::TrajectoryReadEvent, PickModeMoveRep::translate, PickModeMoveFragment::translate, PickModeMoveResidue::translate, STLDisplayDevice::triangle, RadianceDisplayDevice::triangle, tricolor_intersect, FileRenderer::trimesh_c3f_n3f_v3f, X3DDisplayDevice::trimesh_c4n3v3, Vrml2DisplayDevice::trimesh_c4n3v3, X3DDisplayDevice::trimesh_c4u_n3b_v3f, WavefrontDisplayDevice::trimesh_c4u_n3b_v3f, Vrml2DisplayDevice::trimesh_c4u_n3b_v3f, TachyonDisplayDevice::trimesh_c4u_n3b_v3f, RenderManDisplayDevice::trimesh_c4u_n3b_v3f, POV3DisplayDevice::trimesh_c4u_n3b_v3f, OSPRayRenderer::trimesh_c4u_n3b_v3f, OSPRayDisplayDevice::trimesh_c4u_n3b_v3f, OSPRay2Renderer::trimesh_c4u_n3b_v3f, OSPRay2DisplayDevice::trimesh_c4u_n3b_v3f, OptiXRenderer::trimesh_c4u_n3b_v3f, OptiXDisplayDevice::trimesh_c4u_n3b_v3f, FileRenderer::trimesh_c4u_n3b_v3f, ANARIRender::trimesh_c4u_n3b_v3f, ANARIDisplayDevice::trimesh_c4u_n3b_v3f, trimesh_c4u_n3b_v3f_intersect, OSPRayRenderer::trimesh_c4u_n3f_v3f, OSPRayDisplayDevice::trimesh_c4u_n3f_v3f, OSPRay2Renderer::trimesh_c4u_n3f_v3f, OSPRay2DisplayDevice::trimesh_c4u_n3f_v3f, OptiXRenderer::trimesh_c4u_n3f_v3f, OptiXDisplayDevice::trimesh_c4u_n3f_v3f, FileRenderer::trimesh_c4u_n3f_v3f, ANARIRender::trimesh_c4u_n3f_v3f, ANARIDisplayDevice::trimesh_c4u_n3f_v3f, OSPRayRenderer::trimesh_n3b_v3f, OSPRayDisplayDevice::trimesh_n3b_v3f, OSPRay2Renderer::trimesh_n3b_v3f, OSPRay2DisplayDevice::trimesh_n3b_v3f, OptiXRenderer::trimesh_n3b_v3f, OptiXDisplayDevice::trimesh_n3b_v3f, FileRenderer::trimesh_n3b_v3f, ANARIRender::trimesh_n3b_v3f, ANARIDisplayDevice::trimesh_n3b_v3f, trimesh_n3b_v3f_intersect, OSPRayRenderer::trimesh_n3f_v3f, OSPRayDisplayDevice::trimesh_n3f_v3f, OSPRay2Renderer::trimesh_n3f_v3f, OSPRay2DisplayDevice::trimesh_n3f_v3f, OptiXRenderer::trimesh_n3f_v3f, OptiXDisplayDevice::trimesh_n3f_v3f, FileRenderer::trimesh_n3f_v3f, ANARIRender::trimesh_n3f_v3f, ANARIDisplayDevice::trimesh_n3f_v3f, trimesh_n3f_v3f_intersect, OptiXDisplayDevice::trimesh_n3fopt_v3f, FileRenderer::trimesh_n3fopt_v3f, trimesh_v3f_intersect, X3DOMDisplayDevice::tristrip, X3DDisplayDevice::tristrip, Vrml2DisplayDevice::tristrip, MoleculeList::unfix, colvarmodule::rvector::unit, PBCControls::update, GraphicsFltkMenu::update_pbc, GraphicsFltkMenu::update_repindex, ToolFltkMenu::update_toolrep_choosers, colvarmodule::vector1d::vector1d, colvar_grid_scalar::vector_gradient_finite_diff, vmd_gaussdensity_avx2, vmd_gaussdensity_opt, vmd_gridsearch_bonds, OpenGLExtensions::vmdQueryExtension, vs_htonl, vs_ntohl, colvarbias_reweightaMD::write_cumulant_expansion_pmf, colvarbias_reweightaMD::write_exponential_reweighted_pmf, RenderManDisplayDevice::write_header, RadianceDisplayDevice::write_header, LibGelatoDisplayDevice::write_header, GelatoDisplayDevice::write_header, UIestimator::UIestimator::write_interal_data, and MolFilePlugin::write_volumetric. |
