NAMD
colvarproxy_namd Member List

This is the complete list of members for colvarproxy_namd, including all inherited members.

add_energy(cvm::real energy)colvarproxy_namd
appForcesGlobalMasterprotected
appForcesChangedGlobalMasterprotected
appliedForces()GlobalMaster
atomIdBeginGlobalMasterprotected
atomIdEndGlobalMasterprotected
atomPositionBeginGlobalMasterprotected
atoms_mapcolvarproxy_namdprotected
backend_angstrom_value()colvarproxy_namdinline
backup_file(char const *filename)colvarproxy_namd
boltzmann()colvarproxy_namdinline
calculate()colvarproxy_namdvirtual
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 classcolvarproxy_namdfriend
dt()colvarproxy_namdinline
error(std::string const &message)colvarproxy_namd
exit(std::string const &message)colvarproxy_namd
fAtomsGlobalMasterprotected
first_timestepcolvarproxy_namdprotected
flush_output_stream(std::ostream *os)colvarproxy_namd
forcedAtoms()GlobalMaster
forceIdBeginGlobalMasterprotected
forceIdEndGlobalMasterprotected
getAtomIdBegin()GlobalMasterprotected
getAtomIdEnd()GlobalMasterprotected
getAtomPositionBegin()GlobalMasterprotected
getForceIdBegin()GlobalMasterprotected
getForceIdEnd()GlobalMasterprotected
getGridObjIndexBegin()GlobalMasterprotected
getGridObjIndexEnd()GlobalMasterprotected
getGridObjValueBegin()GlobalMasterprotected
getGridObjValueEnd()GlobalMasterprotected
getGroupMassBegin()GlobalMasterprotected
getGroupMassEnd()GlobalMasterprotected
getGroupPositionBegin()GlobalMasterprotected
getGroupPositionEnd()GlobalMasterprotected
getGroupTotalForceBegin()GlobalMasterprotected
getGroupTotalForceEnd()GlobalMasterprotected
getLastAtomsForcedBegin()GlobalMasterprotected
getLastAtomsForcedEnd()GlobalMasterprotected
getLastForcesBegin()GlobalMasterprotected
getTotalForce()GlobalMasterprotected
GlobalMaster()GlobalMasterprotected
gridobjForcesGlobalMasterprotected
gridObjForces()GlobalMaster
gridObjIndexBeginGlobalMasterprotected
gridObjIndexEndGlobalMasterprotected
gridObjValueBeginGlobalMasterprotected
gridObjValueEndGlobalMasterprotected
groupForces()GlobalMaster
groupMassBeginGlobalMasterprotected
groupMassEndGlobalMasterprotected
groupPositionBeginGlobalMasterprotected
groupPositionEndGlobalMasterprotected
groupTotalForceBeginGlobalMasterprotected
groupTotalForceEndGlobalMasterprotected
grpForcesGlobalMasterprotected
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_namdprotected
init_volmap(int volmap_id)colvarproxy_namd
init_volmap(const char *volmap_name)colvarproxy_namd
lastAtomsForcedBeginGlobalMasterprotected
lastAtomsForcedEndGlobalMasterprotected
lastForcesBeginGlobalMasterprotected
latticeGlobalMasterprotected
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()GlobalMasterprotected
modifyForcedAtoms()GlobalMasterprotected
modifyGridObjForces()GlobalMasterprotected
modifyGroupForces()GlobalMasterprotected
modifyRequestedAtoms()GlobalMasterprotected
modifyRequestedGridObjects()GlobalMasterprotected
modifyRequestedGroups()GlobalMasterprotected
num_replicas()colvarproxy_namdvirtual
old_num_groups_requestedGlobalMaster
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_stepcolvarproxy_namdprotected
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_namdinline
randomcolvarproxy_namdprotected
reductioncolvarproxy_namdprotected
replica_comm_barrier()colvarproxy_namdvirtual
replica_comm_recv(char *msg_data, int buf_len, int src_rep)colvarproxy_namdvirtual
replica_comm_send(char *msg_data, int msg_len, int dest_rep)colvarproxy_namdvirtual
replica_enabled()colvarproxy_namdvirtual
replica_index()colvarproxy_namdvirtual
reqAtomsGlobalMasterprotected
reqAtomsChangedGlobalMasterprotected
reqGridObjsGlobalMasterprotected
reqGridObjsChangedGlobalMasterprotected
reqGroupsGlobalMasterprotected
reqGroupsChangedGlobalMasterprotected
request_total_force(bool yesno)colvarproxy_namd
requestedAtoms()GlobalMaster
requestedGridObjs()GlobalMaster
requestedGroups()GlobalMaster
requestedTotalForces()GlobalMasterinline
requestTotalForce(bool yesno=true)GlobalMasterinlineprotected
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_namdinline
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)GlobalMasterinline
setup()colvarproxy_namd
simparamscolvarproxy_namdprotected
stepGlobalMaster
temperature()colvarproxy_namdinline
thermostat_temperaturecolvarproxy_namdprotected
total_forces_enabled() const colvarproxy_namdinline
totalForceBeginGlobalMasterprotected
totalForceRequestedGlobalMasterprotected
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()GlobalMasterinlinevirtual