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colvarscript_commands_colvar.h File Reference

Go to the source code of this file.

Functions
	CVSCRIPT (colvar_addforce,"Apply the given force onto this colvar and return the same\n""force:float or array-Applied force;matches colvar dimensionality", 1, 1,"force:float or array-Applied force;must match colvar dimensionality", std::string const f_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv)));std::istringstream is(f_str);is.width(cvm::cv_width);is.precision(cvm::cv_prec);colvarvalue force(this_colvar->value());force.is_derivative();if(force.from_simple_string(is.str())!=COLVARS_OK){script->add_error_msg("addforce:error parsing force value");return COLVARSCRIPT_ERROR;}this_colvar->add_bias_force(force);script->set_result_colvarvalue(force);return COLVARS_OK;) CVSCRIPT(colvar_communicateforces
Communicate bias forces from this colvar to this_colvar	communicate_forces ()
	CVSCRIPT (colvar_cvcflags,"Enable or disable individual components by setting their active flags", 1, 1,"flags:integer array-Zero/nonzero value disables/enables the CVC", std::string const flags_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv)));std::istringstream is(flags_str);std::vector< bool > flags;int flag;while(is >> flag){flags.push_back(flag!=0);}int res=this_colvar->set_cvc_flags(flags);if(res!=COLVARS_OK){script->add_error_msg("Error setting CVC flags");return COLVARSCRIPT_ERROR;}script->set_result_str("0");return COLVARS_OK;) CVSCRIPT(colvar_delete
	CVSCRIPT (colvar_get,"Get the value of the given feature for this colvar\n""state:1/0-State of the given feature", 1, 1,"feature:string-Name of the feature", return script->proc_features(this_colvar, objc, objv);) CVSCRIPT(colvar_getappliedforce
matches the colvar script	set_result_colvarvalue (this_colvar->applied_force())
	CVSCRIPT (colvar_resetbiasforce,"Return the total of the forces applied to this colvar", 0, 0,"", this_colvar->reset_bias_force();return COLVARS_OK;) CVSCRIPT(colvar_getatomgroups
Variables
Communicate bias forces from this colvar to	atoms
return	COLVARS_OK
Delete this	colvar
Delete this along with all biases that depend on	it
Delete this along with all biases that depend on delete	this_colvar
Return the total of the forces applied to this colvar n	force
matches the colvar	dimensionality
Return the atom indices used by this colvar as a list of lists n	groups
Return the atom indices used by this colvar as a list of lists n std::string	result

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Function Documentation

Communicate bias forces from this colvar to this_colvar communicate_forces (    )

CVSCRIPT (  colvar_resetbiasforce   , "Return the total of the forces applied to this colvar"   , 0   , 0   , ""   , this_colvar-   , reset_bias_force();return COLVARS_OK;    )

CVSCRIPT (  colvar_get   , "Get the value of the given feature for this colvar\n""state:1/0-State of the given feature"   , 1   , 1   , "feature:string-Name of the feature"   , return script-   , proc_features(this_colvar, objc, objv);    )

CVSCRIPT (  colvar_cvcflags   , "Enable or disable individual components by setting their active flags"   , 1   , 1   , "flags:integer array-Zero/nonzero value disables/enables the CVC"    )

CVSCRIPT (  colvar_addforce   , "Apply the given force onto this colvar and return the same\n""force:float or array-Applied force;matches colvar dimensionality"   , 1   , 1   , "force:float or array-Applied force;must match colvar dimensionality"    )

matches the colvar script set_result_colvarvalue (  this_colvar-   , applied_force()    )

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Variable Documentation

Communicate bias forces from this colvar to atoms

Definition at line 32 of file colvarscript_commands_colvar.h. Referenced by colvarmodule::atom_group::begin, QuickSurf::calc_surf, copyatomstoconstbuf, cudaenergythread, colvarmodule::atom_group::end, energythread, BaseMolecule::find_atom_in_residue, colvarproxy_vmd::load_atoms, openclenergythread, colvarmodule::atom_group::operator[], TextInterp::pick_selection_cb, TclTextInterp::pick_selection_cb, colvar::cvc::read_data, MolFilePlugin::read_optional_structure, MolFilePlugin::read_structure, colvarmodule::atom_group::reset_atoms_data, GeometryMol::set_pick_selection, colvar::setup, simple_scalar_dist_functions, colvarmodule::atom_group::size, tcl_colvars, vmd_cuda_device_props, vmd_cuda_vol_cpotential, vmd_opencl_vol_cpotential, vol_cpotential, vol_cpotential_cpu, and MolFilePlugin::write_structure.

matches the colvar

Definition at line 77 of file colvarscript_commands_colvar.h. Referenced by colvarmodule::parse_colvars.

return COLVARS_OK

Definition at line 81 of file colvarscript_commands_colvar.h.

matches the colvar dimensionality

Definition at line 77 of file colvarscript_commands_colvar.h.

Return the total of the forces applied to this colvar n force

Definition at line 77 of file colvarscript_commands_colvar.h. Referenced by colvar::add_bias_force, colvar::add_bias_force_actual_value, VRPNFeedback::addforcefield, VRPNFeedback::addplaneconstraint, colvar::map_total::apply_force, colvar::euler_theta::apply_force, colvar::euler_psi::apply_force, colvar::euler_phi::apply_force, colvar::spin_angle::apply_force, colvar::tilt::apply_force, colvar::orientation_proj::apply_force, colvar::orientation_angle::apply_force, colvar::orientation::apply_force, colvar::dihedPC::apply_force, colvar::alpha_angles::apply_force, colvar::cartesian::apply_force, colvar::eigenvector::apply_force, colvar::rmsd::apply_force, colvar::inertia_z::apply_force, colvar::inertia::apply_force, colvar::gyration::apply_force, colvar::dipole_magnitude::apply_force, colvar::distance_pairs::apply_force, colvar::distance_inv::apply_force, colvar::distance_dir::apply_force, colvar::distance_xy::apply_force, colvar::distance_z::apply_force, colvar::distance_vec::apply_force, colvar::distance::apply_force, colvar::groupcoordnum::apply_force, colvar::selfcoordnum::apply_force, colvar::h_bond::apply_force, colvar::coordnum::apply_force, colvar::polar_phi::apply_force, colvar::polar_theta::apply_force, colvar::dihedral::apply_force, colvar::dipole_angle::apply_force, colvar::angle::apply_force, colvar::alch_Flambda::apply_force, glwin_spheremap_update_hmd_warp, IMDMgr::send_forces, Tool::setforcefield, Tool::tug, and colvarbias_restraint_histogram::update.

Return the atom indices used by this colvar as a list of lists n groups

Definition at line 94 of file colvarscript_commands_colvar.h.

Delete this along with all biases that depend on it

Definition at line 60 of file colvarscript_commands_colvar.h. Referenced by VMDDisplayList::first, colvarbias_meta::hill::hill, colvar::init_components, iter_dealloc, iter_len, iter_next, VMDDisplayList::next, wkf_shared_iterator_destroy, wkf_shared_iterator_getfatalerror, wkf_shared_iterator_init, wkf_shared_iterator_next_tile, wkf_shared_iterator_set, wkf_shared_iterator_setfatalerror, and colvar::write_acf.

Return the atom indices used by this colvar as a list of lists n std::string result

Definition at line 94 of file colvarscript_commands_colvar.h. Referenced by access_tcl_atomsel, as_constcharptr, as_int, as_pyint, as_pystring, colvarmodule::quaternion::as_vector, colvarmodule::rvector::as_vector, atomsel_repr, atomselection_subscript, call_callbacks, compute_norm2_stats, contacts, cylinder_array_bounds, cylinder_array_color_bounds, FrameSelector::do_dialog, colvarbias_restraint_linear::energy_difference, colvarbias_restraint_harmonic::energy_difference, colvarproxy_atom_groups::get_num_active_atom_groups, colvarproxy_atoms::get_num_active_atoms, colvarparams::get_param_grad_names, colvarparams::get_param_names, colvarvalue::inner_opt, legacy_atomsel_get, measure_fit, molecule_tcl, colvarvalue::norm2, colvarmodule::vector1d::norm2, OptiXPrintRayStats, OptiXWriteImage, colvarvalue::p2leg_opt, poisson_sample_on_sphere, py_add, py_allmacros, py_atomselect, py_evaltcl, py_fit, py_get, py_get_accessions, py_get_autoupdate, py_get_databases, py_get_filenames, py_get_filetypes, py_get_remarks, py_hbonds, py_imdconnected, py_is_fixed, py_is_shown, py_label_getvalues, py_list_attrs, py_menushow, py_mol_get_volumetric, py_sendforces, py_set_colormap, py_timestep, py_velocities, ring_array_color_bounds, colvarmodule::run_tcl_script, shade_light, shader_template, colvarmodule::vector1d::slice, sphere_array_bounds, sphere_array_color_bounds, colvarmodule::vector1d::sum, colvarproxy_tcl::tcl_run_colvar_callback, TclTextInterp::TclTextInterp, text_cmd_color, text_cmd_label, text_cmd_material, text_cmd_mol, text_cmd_plugin, topo_del_angle, topo_del_bond, topo_del_dihed, topo_del_improper, tricolor_bounds, trimesh_c4u_n3b_v3f_bounds, trimesh_n3b_v3f_bounds, trimesh_n3f_v3f_bounds, trimesh_v3f_bounds, VMDApp::vmd_choose_file, vmd_measure_contacts, vmd_measure_hbonds, VMDTkMenu::where, VMDTkinterMenu::where, and wkf_cond_wait.

Delete this along with all biases that depend on delete this_colvar

Definition at line 60 of file colvarscript_commands_colvar.h.

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