| accelMD_enabled() const override | colvarproxy_namd | inline |
| accelMDOn | colvarproxy_namd | protected |
| add_energy(cvm::real energy) override | colvarproxy_namd | |
| amd_weight_factor | colvarproxy_namd | protected |
| appForces | GlobalMaster | protected |
| appForcesChanged | GlobalMaster | protected |
| appliedForces() | GlobalMaster | |
| atomIdBegin | GlobalMaster | protected |
| atomIdEnd | GlobalMaster | protected |
| atomPositionBegin | GlobalMaster | protected |
| atoms_map | colvarproxy_namd | protected |
| backup_file(char const *filename) override | colvarproxy_namd | |
| calculate() | colvarproxy_namd | virtual |
| changedAtoms() | GlobalMaster | |
| changedForces() | GlobalMaster | |
| changedGridObjs() | GlobalMaster | |
| changedGroups() | GlobalMaster | |
| check() const | GlobalMaster | |
| check_atom_id(int atom_number) override | colvarproxy_namd | |
| check_atom_id(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override | colvarproxy_namd | |
| check_atom_name_selections_available() override | colvarproxy_namd | |
| check_replicas_enabled() override | colvarproxy_namd | |
| check_volmap_by_id(int volmap_id) override | colvarproxy_namd | |
| check_volmap_by_name(char const *volmap_name) override | colvarproxy_namd | |
| check_volmaps_available() override | colvarproxy_namd | |
| clear_atom(int index) override | colvarproxy_namd | |
| clear_atom_group(int index) override | colvarproxy_namd | |
| clear_volmap(int index) override | colvarproxy_namd | |
| clearChanged() | GlobalMaster | |
| close_output_stream(std::string const &output_name) override | colvarproxy_namd | |
| close_output_streams() override | colvarproxy_namd | |
| colvarproxy_namd() | colvarproxy_namd | |
| compute_volmap(int flags, int volmap_id, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real *value, cvm::real *atom_field) override | colvarproxy_namd | |
| cvm::atom class | colvarproxy_namd | friend |
| error(std::string const &message) override | colvarproxy_namd | |
| fAtoms | GlobalMaster | protected |
| first_timestep | colvarproxy_namd | protected |
| flush_output_stream(std::string const &output_name) override | colvarproxy_namd | |
| flush_output_streams() override | colvarproxy_namd | |
| forcedAtoms() | GlobalMaster | |
| forceIdBegin | GlobalMaster | protected |
| forceIdEnd | GlobalMaster | protected |
| get_accelMD_factor() const override | colvarproxy_namd | inline |
| get_volmap_id_from_name(char const *volmap_name) override | colvarproxy_namd | |
| getAtomIdBegin() | GlobalMaster | protected |
| getAtomIdEnd() | GlobalMaster | protected |
| getAtomPositionBegin() | GlobalMaster | protected |
| getForceIdBegin() | GlobalMaster | protected |
| getForceIdEnd() | GlobalMaster | protected |
| getGridForceGridValue(int flags, T const *grid, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real *value, cvm::real *atom_field) | colvarproxy_namd | |
| getGridObjIndexBegin() | GlobalMaster | protected |
| getGridObjIndexEnd() | GlobalMaster | protected |
| getGridObjValueBegin() | GlobalMaster | protected |
| getGridObjValueEnd() | GlobalMaster | protected |
| getGroupMassBegin() | GlobalMaster | protected |
| getGroupMassEnd() | GlobalMaster | protected |
| getGroupPositionBegin() | GlobalMaster | protected |
| getGroupPositionEnd() | GlobalMaster | protected |
| getGroupTotalForceBegin() | GlobalMaster | protected |
| getGroupTotalForceEnd() | GlobalMaster | protected |
| getLastAtomsForcedBegin() | GlobalMaster | protected |
| getLastAtomsForcedEnd() | GlobalMaster | protected |
| getLastForcesBegin() | GlobalMaster | protected |
| getTotalForce() | GlobalMaster | protected |
| GlobalMaster() | GlobalMaster | protected |
| globalMasterStep | GlobalMaster | |
| GridForceGridLoop(T const *g, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real *value, cvm::real *atom_field) | colvarproxy_namd | |
| gridobjForces | GlobalMaster | protected |
| gridObjForces() | GlobalMaster | |
| gridObjIndexBegin | GlobalMaster | protected |
| gridObjIndexEnd | GlobalMaster | protected |
| gridObjValueBegin | GlobalMaster | protected |
| gridObjValueEnd | GlobalMaster | protected |
| groupForces() | GlobalMaster | |
| groupMassBegin | GlobalMaster | protected |
| groupMassEnd | GlobalMaster | protected |
| groupPositionBegin | GlobalMaster | protected |
| groupPositionEnd | GlobalMaster | protected |
| groupTotalForceBegin | GlobalMaster | protected |
| groupTotalForceEnd | GlobalMaster | protected |
| grpForces | GlobalMaster | protected |
| init_atom(int atom_number) override | colvarproxy_namd | |
| init_atom(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override | colvarproxy_namd | |
| init_atom_group(std::vector< int > const &atoms_ids) override | colvarproxy_namd | |
| init_atoms_map() | colvarproxy_namd | |
| init_tcl_pointers() override | colvarproxy_namd | |
| init_volmap_by_id(int volmap_id) override | colvarproxy_namd | |
| init_volmap_by_name(const char *volmap_name) override | colvarproxy_namd | |
| lastAtomsForcedBegin | GlobalMaster | protected |
| lastAtomsForcedEnd | GlobalMaster | protected |
| lastForcesBegin | GlobalMaster | protected |
| lattice | GlobalMaster | protected |
| load_atoms_pdb(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double const pdb_field_value) override | colvarproxy_namd | |
| load_coords_pdb(char const *filename, std::vector< cvm::atom_pos > &pos, const std::vector< int > &indices, std::string const &pdb_field, double const pdb_field_value) override | colvarproxy_namd | |
| log(std::string const &message) override | colvarproxy_namd | |
| modifyAppliedForces() | GlobalMaster | protected |
| modifyForcedAtoms() | GlobalMaster | protected |
| modifyGridObjForces() | GlobalMaster | protected |
| modifyGroupForces() | GlobalMaster | protected |
| modifyRequestedAtoms() | GlobalMaster | protected |
| modifyRequestedGridObjects() | GlobalMaster | protected |
| modifyRequestedGroups() | GlobalMaster | protected |
| num_replicas() override | colvarproxy_namd | |
| old_num_groups_requested | GlobalMaster | |
| output_stream(std::string const &output_name, std::string const description) override | colvarproxy_namd | |
| position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const | colvarproxy_namd | |
| previous_NAMD_step | colvarproxy_namd | protected |
| processData(AtomIDList::iterator a_i, AtomIDList::iterator a_e, PositionList::iterator p_i, PositionList::iterator g_i, PositionList::iterator g_e, BigRealList::iterator gm_i, BigRealList::iterator gm_e, ForceList::iterator gtf_i, ForceList::iterator gtf_e, IntList::iterator goi_i, IntList::iterator goi_e, BigRealList::iterator gov_i, BigRealList::iterator gov_e, AtomIDList::iterator last_atoms_forced_i, AtomIDList::iterator last_atoms_forced_e, ForceList::iterator last_forces_i, AtomIDList::iterator, AtomIDList::iterator, ForceList::iterator) | GlobalMaster | |
| rand_gaussian() override | colvarproxy_namd | inline |
| random | colvarproxy_namd | protected |
| reduction | colvarproxy_namd | protected |
| replica_comm_barrier() override | colvarproxy_namd | |
| replica_comm_recv(char *msg_data, int buf_len, int src_rep) override | colvarproxy_namd | |
| replica_comm_send(char *msg_data, int msg_len, int dest_rep) override | colvarproxy_namd | |
| replica_index() override | colvarproxy_namd | |
| reqAtoms | GlobalMaster | protected |
| reqAtomsChanged | GlobalMaster | protected |
| reqGridObjs | GlobalMaster | protected |
| reqGridObjsChanged | GlobalMaster | protected |
| reqGroups | GlobalMaster | protected |
| reqGroupsChanged | GlobalMaster | protected |
| request_total_force(bool yesno) override | colvarproxy_namd | |
| requestedAtoms() | GlobalMaster | |
| requestedGridObjs() | GlobalMaster | |
| requestedGroups() | GlobalMaster | |
| requestedTotalForces() | GlobalMaster | inline |
| requestTotalForce(bool yesno=true) | GlobalMaster | inlineprotected |
| reset() override | colvarproxy_namd | |
| run_colvar_callback(std::string const &name, std::vector< const colvarvalue *> const &cvcs, colvarvalue &value) override | colvarproxy_namd | |
| run_colvar_gradient_callback(std::string const &name, std::vector< const colvarvalue *> const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient) override | colvarproxy_namd | |
| run_force_callback() override | colvarproxy_namd | |
| scalable_group_coms() override | colvarproxy_namd | inline |
| set_unit_system(std::string const &units_in, bool check_only) override | colvarproxy_namd | |
| setLattice(const Lattice *lat) | GlobalMaster | inline |
| setup() override | colvarproxy_namd | |
| simparams | colvarproxy_namd | protected |
| step | GlobalMaster | |
| total_forces_enabled() const override | colvarproxy_namd | inline |
| totalForceBegin | GlobalMaster | protected |
| totalForceRequested | GlobalMaster | protected |
| update_accelMD_info() | colvarproxy_namd | protected |
| update_atom_properties(int index) | colvarproxy_namd | |
| update_atoms_map(AtomIDList::const_iterator begin, AtomIDList::const_iterator end) | colvarproxy_namd | |
| update_group_properties(int index) | colvarproxy_namd | |
| update_target_temperature() | colvarproxy_namd | |
| ~colvarproxy_namd() | colvarproxy_namd | |
| ~GlobalMaster() | GlobalMaster | inlinevirtual |
