colvarproxy_namd Member List

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

accelMD_enabled() const override (defined in colvarproxy_namd)	colvarproxy_namd	inlinevirtual
accelMDOn	colvarproxy_namd	protected
add_atom_group_slot(int atom_group_id)	colvarproxy_atom_groups	protected
add_atom_slot(int atom_id)	colvarproxy_atoms	protected
add_config(std::string const &cmd, std::string const &conf)	colvarproxy
add_energy(cvm::real energy) override	colvarproxy_namd	virtual
add_error_msg(std::string const &message)	colvarproxy
add_volmap_slot(int volmap_id)	colvarproxy_volmaps
amd_weight_factor (defined in colvarproxy_namd)	colvarproxy_namd	protected
angstrom_to_internal(cvm::real l) const	colvarproxy_system	inline
angstrom_value_	colvarproxy_system	protected
apply_atom_force(int index, cvm::rvector const &new_force)	colvarproxy_atoms	inline
apply_atom_group_force(int index, cvm::rvector const &new_force)	colvarproxy_atom_groups	inline
apply_force_dE_dlambda(cvm::real *force)	colvarproxy_system	virtual
apply_volmap_force(int index, cvm::real const &new_force)	colvarproxy_volmaps	inline
atom_groups_charges	colvarproxy_atom_groups	protected
atom_groups_coms	colvarproxy_atom_groups	protected
atom_groups_ids	colvarproxy_atom_groups	protected
atom_groups_masses	colvarproxy_atom_groups	protected
atom_groups_max_applied_force_	colvarproxy_atom_groups	protected
atom_groups_new_colvar_forces	colvarproxy_atom_groups	protected
atom_groups_refcount	colvarproxy_atom_groups	protected
atom_groups_rms_applied_force_	colvarproxy_atom_groups	protected
atom_groups_total_forces	colvarproxy_atom_groups	protected
atoms_charges	colvarproxy_atoms	protected
atoms_ids	colvarproxy_atoms	protected
atoms_map	colvarproxy_namd	protected
atoms_masses	colvarproxy_atoms	protected
atoms_max_applied_force_	colvarproxy_atoms	protected
atoms_max_applied_force_id_	colvarproxy_atoms	protected
atoms_new_colvar_forces	colvarproxy_atoms	protected
atoms_positions	colvarproxy_atoms	protected
atoms_refcount	colvarproxy_atoms	protected
atoms_rms_applied_force_	colvarproxy_atoms	protected
atoms_total_forces	colvarproxy_atoms	protected
b_delete_requested	colvarproxy	protected
b_simulation_continuing	colvarproxy	protected
b_simulation_running	colvarproxy	protected
b_smp_active	colvarproxy_smp
backup_file(char const *filename) override	colvarproxy_namd	virtual
colvarproxy::backup_file(std::string const &filename)	colvarproxy_io	inline
boltzmann() const	colvarproxy_system	inline
boltzmann_	colvarproxy_system	protected
boundaries_non_periodic enum value (defined in colvarproxy_system)	colvarproxy_system	protected
boundaries_pbc_ortho enum value (defined in colvarproxy_system)	colvarproxy_system	protected
boundaries_pbc_triclinic enum value (defined in colvarproxy_system)	colvarproxy_system	protected
boundaries_type	colvarproxy_system	protected
Boundaries_type enum name	colvarproxy_system	protected
boundaries_unsupported enum value (defined in colvarproxy_system)	colvarproxy_system	protected
cached_alch_lambda	colvarproxy_system	protected
cached_alch_lambda_changed	colvarproxy_system	protected
calculate() (defined in colvarproxy_namd)	colvarproxy_namd
check_atom_id(int atom_number) override	colvarproxy_namd	virtual
check_atom_id(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override	colvarproxy_namd	virtual
check_atom_name_selections_available() override	colvarproxy_namd	virtual
check_smp_enabled()	colvarproxy_smp	virtual
check_volmap_by_id(int volmap_id) override	colvarproxy_namd	virtual
check_volmap_by_name(char const *volmap_name) override	colvarproxy_namd	virtual
colvarproxy::check_volmap_by_name(std::string const &volmap_name)	colvarproxy_volmaps
check_volmaps_available() override	colvarproxy_namd	virtual
clear_atom(int index) override	colvarproxy_namd	virtual
clear_atom_group(int index) override	colvarproxy_namd	virtual
clear_error_msgs()	colvarproxy
clear_volmap(int index) override	colvarproxy_namd	virtual
close_input_stream(std::string const &input_name)	colvarproxy_io
close_input_streams()	colvarproxy_io
close_output_stream(std::string const &output_name) override	colvarproxy_namd	virtual
close_output_streams() override	colvarproxy_namd	virtual
colvarproxy()	colvarproxy
colvarproxy_atom_groups()	colvarproxy_atom_groups
colvarproxy_atoms()	colvarproxy_atoms
colvarproxy_io()	colvarproxy_io
colvarproxy_namd() (defined in colvarproxy_namd)	colvarproxy_namd
colvarproxy_replicas()	colvarproxy_replicas
colvarproxy_script()	colvarproxy_script
colvarproxy_smp()	colvarproxy_smp
colvarproxy_system()	colvarproxy_system
colvarproxy_tcl()	colvarproxy_tcl
colvarproxy_volmaps()	colvarproxy_volmaps
colvars	colvarproxy
compute_max_atom_groups_applied_force()	colvarproxy_atom_groups
compute_max_atoms_applied_force()	colvarproxy_atoms
compute_max_volmaps_applied_force()	colvarproxy_volmaps
compute_rms_atom_groups_applied_force()	colvarproxy_atom_groups
compute_rms_atoms_applied_force()	colvarproxy_atoms
compute_rms_volmaps_applied_force()	colvarproxy_volmaps
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	virtual
config_queue_	colvarproxy	protected
cvm::atom (defined in colvarproxy_namd)	colvarproxy_namd	friend
default_restart_frequency() const	colvarproxy_io	inline
delete_input_stream(std::string const &input_name)	colvarproxy_io
delete_requested() const	colvarproxy	inline
dt() const	colvarproxy_system	inline
end_of_step()	colvarproxy
engine_name() const (defined in colvarproxy)	colvarproxy	inline
engine_name_	colvarproxy	protected
engine_ready() const	colvarproxy	inline
engine_ready_	colvarproxy	protected
error(std::string const &message) override	colvarproxy_namd	virtual
error_output	colvarproxy	protected
features_hash	colvarproxy	protected
first_timestep (defined in colvarproxy_namd)	colvarproxy_namd	protected
flush_output_stream(std::string const &output_name) override	colvarproxy_namd	virtual
flush_output_streams() override	colvarproxy_namd	virtual
get_accelMD_factor() const override	colvarproxy_namd	inlinevirtual
get_alch_lambda(cvm::real *lambda)	colvarproxy_system	virtual
get_atom_applied_forces() const (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
get_atom_charge(int index) const	colvarproxy_atoms	inline
get_atom_charges() (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
get_atom_group_charge(int index) const	colvarproxy_atom_groups	inline
get_atom_group_com(int index) const	colvarproxy_atom_groups	inline
get_atom_group_id(int index) const	colvarproxy_atom_groups	inline
get_atom_group_ids() const (defined in colvarproxy_atom_groups)	colvarproxy_atom_groups	inline
get_atom_group_mass(int index) const	colvarproxy_atom_groups	inline
get_atom_group_total_force(int index) const	colvarproxy_atom_groups	inline
get_atom_group_velocity(int)	colvarproxy_atom_groups	inline
get_atom_id(int index) const	colvarproxy_atoms	inline
get_atom_ids() const (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
get_atom_mass(int index) const	colvarproxy_atoms	inline
get_atom_masses() const (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
get_atom_position(int index) const	colvarproxy_atoms	inline
get_atom_positions() const (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
get_atom_total_force(int index) const	colvarproxy_atoms	inline
get_atom_total_forces() const (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
get_atom_velocity(int)	colvarproxy_atoms	inline
get_d2E_dlambda2(cvm::real *d2E_dlambda2)	colvarproxy_system	virtual
get_dE_dlambda(cvm::real *dE_dlambda)	colvarproxy_system	virtual
get_error_msgs()	colvarproxy
get_frame(long int &)	colvarproxy_io	virtual
get_molid(int &molid)	colvarproxy_system	virtual
get_num_active_atom_groups() const	colvarproxy_atom_groups
get_num_active_atoms() const	colvarproxy_atoms
get_tcl_interp()	colvarproxy_tcl	inline
get_version_from_string(char const *version_string)	colvarproxy
get_volmap_id(int index) const	colvarproxy_volmaps	inline
get_volmap_id_from_name(char const *volmap_name) override	colvarproxy_namd	virtual
get_volmap_value(int index) const	colvarproxy_volmaps	inline
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
GridForceGridLoop(T const *g, cvm::atom_iter atom_begin, cvm::atom_iter atom_end, cvm::real *value, cvm::real *atom_field)	colvarproxy_namd
have_scripts	colvarproxy_script
increase_refcount(int index)	colvarproxy_atoms	inline
indirect_lambda_biasing_force	colvarproxy_system
init_atom(int atom_number) override	colvarproxy_namd	virtual
init_atom(cvm::residue_id const &residue, std::string const &atom_name, std::string const &segment_id) override	colvarproxy_namd	virtual
init_atom_group(std::vector< int > const &atoms_ids) override	colvarproxy_namd	virtual
init_atoms_map()	colvarproxy_namd
init_tcl_pointers() override	colvarproxy_namd	virtual
init_volmap_by_id(int volmap_id) override	colvarproxy_namd	virtual
init_volmap_by_name(const char *volmap_name) override	colvarproxy_namd	virtual
colvarproxy::init_volmap_by_name(std::string const &volmap_name)	colvarproxy_volmaps
input_prefix() const	colvarproxy_io	inline
input_prefix_str	colvarproxy_io	protected
input_stream(std::string const &input_name, std::string const description="file/channel", bool error_on_fail=true)	colvarproxy_io
input_stream_error_	colvarproxy_io	protected
input_stream_exists(std::string const &input_name)	colvarproxy_io
input_stream_from_string(std::string const &input_name, std::string const &content, std::string const description="string")	colvarproxy_io
input_streams_	colvarproxy_io	protected
internal_to_angstrom(cvm::real l) const	colvarproxy_system	inline
io_available() override	colvarproxy	virtual
kcal_mol_value_	colvarproxy_system	protected
list_input_stream_names() const	colvarproxy_io
load_atoms_pdb(char const *filename, cvm::atom_group &atoms, std::string const &pdb_field, double const pdb_field_value) override	colvarproxy_namd	virtual
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	virtual
log(std::string const &message) override	colvarproxy_namd	virtual
max_atom_groups_applied_force() const	colvarproxy_atom_groups	inline
max_atoms_applied_force() const	colvarproxy_atoms	inline
max_atoms_applied_force_id() const	colvarproxy_atoms	inline
modified_atom_list() const	colvarproxy_atoms	inline
modified_atom_list_	colvarproxy_atoms	protected
modify_atom_applied_forces() (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
modify_atom_charges() (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
modify_atom_group_applied_forces() (defined in colvarproxy_atom_groups)	colvarproxy_atom_groups	inline
modify_atom_group_charges() (defined in colvarproxy_atom_groups)	colvarproxy_atom_groups	inline
modify_atom_group_masses() (defined in colvarproxy_atom_groups)	colvarproxy_atom_groups	inline
modify_atom_group_positions() (defined in colvarproxy_atom_groups)	colvarproxy_atom_groups	inline
modify_atom_group_total_forces() (defined in colvarproxy_atom_groups)	colvarproxy_atom_groups	inline
modify_atom_masses() (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
modify_atom_positions() (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
modify_atom_total_forces() (defined in colvarproxy_atoms)	colvarproxy_atoms	inline
num_replicas() override	colvarproxy_namd	virtual
omp_lock_state	colvarproxy_smp	protected
output_prefix() const	colvarproxy_io	inline
output_prefix_str	colvarproxy_io	protected
output_stream(std::string const &output_name, std::string const description) override	colvarproxy_namd	virtual
output_stream_error_	colvarproxy_io	protected
output_stream_exists(std::string const &output_name)	colvarproxy_io	virtual
output_streams_	colvarproxy_io	protected
parse_module_config()	colvarproxy	virtual
position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const	colvarproxy_namd	virtual
post_run()	colvarproxy
previous_NAMD_step (defined in colvarproxy_namd)	colvarproxy_namd	protected
print_input_atomic_data()	colvarproxy
print_output_atomic_data()	colvarproxy
rand_gaussian() override	colvarproxy_namd	inlinevirtual
random	colvarproxy_namd	protected
reciprocal_cell_x	colvarproxy_system	protected
reciprocal_cell_y (defined in colvarproxy_system)	colvarproxy_system	protected
reciprocal_cell_z (defined in colvarproxy_system)	colvarproxy_system	protected
reduction	colvarproxy_namd	protected
remove_file(char const *filename)	colvarproxy_io	virtual
remove_file(std::string const &filename)	colvarproxy_io	inline
rename_file(char const *filename, char const *newfilename)	colvarproxy_io	virtual
rename_file(std::string const &filename, std::string const &newfilename)	colvarproxy_io	inline
replica_comm_barrier() override	colvarproxy_namd	virtual
replica_comm_recv(char *msg_data, int buf_len, int src_rep) override	colvarproxy_namd	virtual
replica_comm_send(char *msg_data, int msg_len, int dest_rep) override	colvarproxy_namd	virtual
replica_enabled() override	colvarproxy_namd	virtual
replica_index() override	colvarproxy_namd	virtual
request_deletion()	colvarproxy	virtual
request_total_force(bool yesno) override	colvarproxy_namd	virtual
reset() override	colvarproxy_namd	virtual
reset_modified_atom_list()	colvarproxy_atoms	inline
reset_pbc_lattice()	colvarproxy_system
restart_frequency_engine	colvarproxy_io	protected
restart_output_prefix() const	colvarproxy_io	inline
restart_output_prefix_str	colvarproxy_io	protected
rms_atom_groups_applied_force() const	colvarproxy_atom_groups	inline
rms_atoms_applied_force() const	colvarproxy_atoms	inline
run_colvar_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value) override (defined in colvarproxy_namd)	colvarproxy_namd	virtual
run_colvar_gradient_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient) override (defined in colvarproxy_namd)	colvarproxy_namd	virtual
run_force_callback() override	colvarproxy_namd	virtual
scalable_group_coms() override	colvarproxy_namd	inlinevirtual
script	colvarproxy_script
send_alch_lambda()	colvarproxy_system	virtual
set_alch_lambda(cvm::real lambda)	colvarproxy_system
set_default_restart_frequency(int freq)	colvarproxy_io	virtual
set_frame(long int)	colvarproxy_io	virtual
set_input_prefix(std::string const &prefix)	colvarproxy_io	virtual
set_integration_timestep(cvm::real dt)	colvarproxy_system	virtual
set_output_prefix(std::string const &prefix)	colvarproxy_io	virtual
set_restart_output_prefix(std::string const &prefix)	colvarproxy_io	virtual
set_target_temperature(cvm::real T)	colvarproxy_system	virtual
set_tcl_interp(Tcl_Interp *interp)	colvarproxy_tcl	inline
set_unit_system(std::string const &units_in, bool check_only) override	colvarproxy_namd	virtual
setup() override	colvarproxy_namd	virtual
simparams	colvarproxy_namd	protected
simulation_continuing() const	colvarproxy	inline
simulation_running() const	colvarproxy	inline
smp_biases_loop()	colvarproxy_smp	virtual
smp_biases_script_loop()	colvarproxy_smp	virtual
smp_colvars_loop()	colvarproxy_smp	virtual
smp_lock()	colvarproxy_smp	virtual
smp_num_threads()	colvarproxy_smp	virtual
smp_thread_id()	colvarproxy_smp	virtual
smp_trylock()	colvarproxy_smp	virtual
smp_unlock()	colvarproxy_smp	virtual
target_temperature() const	colvarproxy_system	inline
target_temperature_	colvarproxy_system	protected
tcl_available()	colvarproxy_tcl	inline
tcl_get_str(void *obj)	colvarproxy_tcl
tcl_interp_	colvarproxy_tcl	protected
tcl_run_colvar_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, colvarvalue &value)	colvarproxy_tcl
tcl_run_colvar_gradient_callback(std::string const &name, std::vector< const colvarvalue * > const &cvcs, std::vector< cvm::matrix2d< cvm::real > > &gradient)	colvarproxy_tcl
tcl_run_file(std::string const &fileName) (defined in colvarproxy_tcl)	colvarproxy_tcl
tcl_run_force_callback()	colvarproxy_tcl
tcl_run_script(std::string const &script) (defined in colvarproxy_tcl)	colvarproxy_tcl
timestep_	colvarproxy_system	protected
total_force_requested	colvarproxy_system	protected
total_forces_enabled() const override	colvarproxy_namd	inlinevirtual
total_forces_same_step() const	colvarproxy_system	virtual
unit_cell_x	colvarproxy_system	protected
unit_cell_y (defined in colvarproxy_system)	colvarproxy_system	protected
unit_cell_z (defined in colvarproxy_system)	colvarproxy_system	protected
units	colvarproxy_system
update_accelMD_info() (defined in colvarproxy_namd)	colvarproxy_namd	protected
update_atom_properties(int index) (defined in colvarproxy_namd)	colvarproxy_namd
update_atoms_map(AtomIDList::const_iterator begin, AtomIDList::const_iterator end) (defined in colvarproxy_namd)	colvarproxy_namd
update_group_properties(int index) (defined in colvarproxy_namd)	colvarproxy_namd
update_input()	colvarproxy	virtual
update_output()	colvarproxy	virtual
update_pbc_lattice()	colvarproxy_system
update_target_temperature()	colvarproxy_namd
updated_charges() const	colvarproxy_atoms	inline
updated_charges_ (defined in colvarproxy_atoms)	colvarproxy_atoms	protected
updated_masses() const	colvarproxy_atoms	inline
updated_masses_	colvarproxy_atoms	protected
version_int	colvarproxy	protected
version_number() const	colvarproxy	inline
volmap_flag_gradients enum value (defined in colvarproxy_volmaps)	colvarproxy_volmaps
volmap_flag_null enum value (defined in colvarproxy_volmaps)	colvarproxy_volmaps
volmap_flag_use_atom_field enum value (defined in colvarproxy_volmaps)	colvarproxy_volmaps
volmaps_ids	colvarproxy_volmaps	protected
volmaps_max_applied_force_	colvarproxy_volmaps	protected
volmaps_new_colvar_forces	colvarproxy_volmaps	protected
volmaps_refcount	colvarproxy_volmaps	protected
volmaps_rms_applied_force_	colvarproxy_volmaps	protected
volmaps_values	colvarproxy_volmaps	protected
~colvarproxy() override	colvarproxy
~colvarproxy_atom_groups()	colvarproxy_atom_groups	virtual
~colvarproxy_atoms()	colvarproxy_atoms	virtual
~colvarproxy_io()	colvarproxy_io	virtual
~colvarproxy_namd() (defined in colvarproxy_namd)	colvarproxy_namd
~colvarproxy_replicas()	colvarproxy_replicas	virtual
~colvarproxy_script()	colvarproxy_script	virtual
~colvarproxy_smp()	colvarproxy_smp	virtual
~colvarproxy_system()	colvarproxy_system	virtual
~colvarproxy_tcl()	colvarproxy_tcl	virtual
~colvarproxy_volmaps()	colvarproxy_volmaps	virtual