add_energy(cvm::real energy) | colvarproxy_namd | |
appForces | GlobalMaster | protected |
appForcesChanged | GlobalMaster | protected |
appliedForces() | GlobalMaster | |
atomIdBegin | GlobalMaster | protected |
atomIdEnd | GlobalMaster | protected |
atomPositionBegin | GlobalMaster | protected |
atoms_map | colvarproxy_namd | protected |
backend_angstrom_value() | colvarproxy_namd | inline |
backup_file(char const *filename) | colvarproxy_namd | |
boltzmann() | colvarproxy_namd | inline |
calculate() | colvarproxy_namd | virtual |
changedAtoms() | GlobalMaster | |
changedForces() | GlobalMaster | |
changedGridObjs() | GlobalMaster | |
changedGroups() | GlobalMaster | |
check() const | GlobalMaster | |
check_atom_id(int atom_number) | colvarproxy_namd | |
check_atom_id(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) | colvarproxy_namd | |
clear_atom(int index) | colvarproxy_namd | |
clear_atom_group(int index) | colvarproxy_namd | |
clear_volmap(int index) | colvarproxy_namd | |
clearChanged() | GlobalMaster | |
close_output_stream(std::string const &output_name) | colvarproxy_namd | |
colvarproxy_namd() | colvarproxy_namd | |
cvm::atom class | colvarproxy_namd | friend |
dt() | colvarproxy_namd | inline |
error(std::string const &message) | colvarproxy_namd | |
exit(std::string const &message) | colvarproxy_namd | |
fAtoms | GlobalMaster | protected |
first_timestep | colvarproxy_namd | protected |
flush_output_stream(std::ostream *os) | colvarproxy_namd | |
forcedAtoms() | GlobalMaster | |
forceIdBegin | GlobalMaster | protected |
forceIdEnd | GlobalMaster | protected |
getAtomIdBegin() | GlobalMaster | protected |
getAtomIdEnd() | GlobalMaster | protected |
getAtomPositionBegin() | GlobalMaster | protected |
getForceIdBegin() | GlobalMaster | protected |
getForceIdEnd() | GlobalMaster | protected |
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 |
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) | colvarproxy_namd | |
init_atom(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) | colvarproxy_namd | |
init_atom_group(std::vector< int > const &atoms_ids) | colvarproxy_namd | |
init_tcl_pointers() | colvarproxy_namd | protected |
init_volmap(int volmap_id) | colvarproxy_namd | |
init_volmap(const char *volmap_name) | colvarproxy_namd | |
lastAtomsForcedBegin | GlobalMaster | protected |
lastAtomsForcedEnd | GlobalMaster | protected |
lastForcesBegin | GlobalMaster | protected |
lattice | GlobalMaster | protected |
load_atoms(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double const pdb_field_value=0.0) | colvarproxy_namd | |
load_coords(char const *filename, std::vector< cvm::atom_pos > &pos, const std::vector< int > &indices, std::string const &pdb_field, double const pdb_field_value=0.0) | colvarproxy_namd | |
log(std::string const &message) | 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() | colvarproxy_namd | virtual |
old_num_groups_requested | GlobalMaster | |
output_stream(std::string const &output_name, std::ios_base::openmode mode) | 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() | colvarproxy_namd | inline |
random | colvarproxy_namd | protected |
reduction | colvarproxy_namd | protected |
replica_comm_barrier() | colvarproxy_namd | virtual |
replica_comm_recv(char *msg_data, int buf_len, int src_rep) | colvarproxy_namd | virtual |
replica_comm_send(char *msg_data, int msg_len, int dest_rep) | colvarproxy_namd | virtual |
replica_enabled() | colvarproxy_namd | virtual |
replica_index() | colvarproxy_namd | virtual |
reqAtoms | GlobalMaster | protected |
reqAtomsChanged | GlobalMaster | protected |
reqGridObjs | GlobalMaster | protected |
reqGridObjsChanged | GlobalMaster | protected |
reqGroups | GlobalMaster | protected |
reqGroupsChanged | GlobalMaster | protected |
request_total_force(bool yesno) | colvarproxy_namd | |
requestedAtoms() | GlobalMaster | |
requestedGridObjs() | GlobalMaster | |
requestedGroups() | GlobalMaster | |
requestedTotalForces() | GlobalMaster | inline |
requestTotalForce(bool yesno=true) | GlobalMaster | inlineprotected |
reset() | colvarproxy_namd | |
run_colvar_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value) | colvarproxy_namd | |
run_colvar_gradient_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient) | colvarproxy_namd | |
run_force_callback() | colvarproxy_namd | |
scalable_group_coms() | colvarproxy_namd | inline |
script_obj_to_str(unsigned char *obj) | colvarproxy_namd | |
script_obj_to_str_vector(unsigned char *obj) | colvarproxy_namd | |
set_unit_system(std::string const &units_in, bool check_only) | colvarproxy_namd | |
setLattice(const Lattice *lat) | GlobalMaster | inline |
setup() | colvarproxy_namd | |
simparams | colvarproxy_namd | protected |
step | GlobalMaster | |
temperature() | colvarproxy_namd | inline |
thermostat_temperature | colvarproxy_namd | protected |
total_forces_enabled() const | colvarproxy_namd | inline |
totalForceBegin | GlobalMaster | protected |
totalForceRequested | GlobalMaster | 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 | |
~colvarproxy_namd() | colvarproxy_namd | |
~GlobalMaster() | GlobalMaster | inlinevirtual |