acos(real const &x) | colvarmodule | [inline, static] |
analyze() | colvarmodule | |
append_new_config(std::string const &conf) | colvarmodule | |
asin(real const &x) | colvarmodule | [inline, static] |
atan2(real const &x, real const &y) | colvarmodule | [inline, static] |
atom class | colvarmodule | [friend] |
atom_const_iter typedef | colvarmodule | |
atom_group class | colvarmodule | [friend] |
atom_group_by_name(std::string const &name) | colvarmodule | [static] |
atom_iter typedef | colvarmodule | |
atom_pos typedef | colvarmodule | |
backup_file(char const *filename) | colvarmodule | [static] |
bias_by_name(std::string const &name) | colvarmodule | [static] |
biases | colvarmodule | |
biases_active() | colvarmodule | |
calc() | colvarmodule | |
calc_biases() | colvarmodule | |
calc_colvars() | colvarmodule | |
calc_scripted_forces() | colvarmodule | |
change_configuration(std::string const &bias_name, std::string const &conf) | colvarmodule | |
cite_feature(std::string const &feature) | colvarmodule | |
clear_error() | colvarmodule | [static] |
close_traj_file() | colvarmodule | |
colvar_by_name(std::string const &name) | colvarmodule | [static] |
colvarmodule(colvarproxy *proxy) | colvarmodule | |
colvarproxy class | colvarmodule | [friend] |
colvarscript class | colvarmodule | [friend] |
config_changed() | colvarmodule | |
cos(real const &x) | colvarmodule | [inline, static] |
cv_prec | colvarmodule | [static] |
cv_traj_freq | colvarmodule | [static] |
cv_traj_name | colvarmodule | [protected] |
cv_traj_write_labels | colvarmodule | [protected] |
cv_width | colvarmodule | [static] |
debug() | colvarmodule | [inline, static] |
debug_gradients_step_size | colvarmodule | [static] |
decrease_depth() | colvarmodule | [static] |
depth() | colvarmodule | [static] |
depth_s | colvarmodule | [protected] |
depth_v | colvarmodule | [protected] |
dt() | colvarmodule | [static] |
en_prec | colvarmodule | [static] |
en_width | colvarmodule | [static] |
end_of_step() | colvarmodule | |
energy_difference(std::string const &bias_name, std::string const &conf) | colvarmodule | |
error(std::string const &message, int code=COLVARS_ERROR) | colvarmodule | [static] |
exp(real const &x) | colvarmodule | [inline, static] |
fabs(real const &x) | colvarmodule | [inline, static] |
feature_report(int flag=0) | colvarmodule | |
floor(real const &x) | colvarmodule | [inline, static] |
get_config() const | colvarmodule | |
get_error() | colvarmodule | [inline, static] |
get_error_bit(int code) | colvarmodule | [static] |
getline(std::istream &is, std::string &line) | colvarmodule | [static] |
increase_depth() | colvarmodule | [static] |
index_file_names | colvarmodule | |
index_group_names | colvarmodule | |
index_groups | colvarmodule | |
integer_power(real const &x, int const n) | colvarmodule | [inline, static] |
it | colvarmodule | [static] |
it_restart | colvarmodule | [static] |
it_width | colvarmodule | [static] |
line_marker | colvarmodule | [static] |
load_atoms(char const *filename, atom_group &atoms, std::string const &pdb_field, double pdb_field_value=0.0) | colvarmodule | [static] |
load_coords(char const *filename, std::vector< rvector > *pos, atom_group *atoms, std::string const &pdb_field, double pdb_field_value=0.0) | colvarmodule | [static] |
load_coords_xyz(char const *filename, std::vector< rvector > *pos, atom_group *atoms) | colvarmodule | |
log(std::string const &message, int min_log_level=10) | colvarmodule | [static] |
log_default_params() | colvarmodule | [inline, static] |
log_init_messages() | colvarmodule | [inline, static] |
log_input_files() | colvarmodule | [inline, static] |
log_level() | colvarmodule | [inline, static] |
log_output_files() | colvarmodule | [inline, static] |
log_user_params() | colvarmodule | [inline, static] |
logn(real const &x) | colvarmodule | [inline, static] |
main() | colvarmodule | [static] |
num_biases() const | colvarmodule | |
num_biases_feature(int feature_id) const | colvarmodule | |
num_biases_type(std::string const &type) const | colvarmodule | |
num_variables() const | colvarmodule | |
num_variables_feature(int feature_id) const | colvarmodule | |
open_traj_file(std::string const &file_name) | colvarmodule | |
output_prefix() | colvarmodule | [inline, static] |
parse | colvarmodule | [protected] |
parse_biases(std::string const &conf) | colvarmodule | |
parse_colvars(std::string const &conf) | colvarmodule | |
parse_config(std::string &conf) | colvarmodule | |
parse_global_params(std::string const &conf) | colvarmodule | |
position_distance(atom_pos const &pos1, atom_pos const &pos2) | colvarmodule | [static] |
pow(real const &x, real const &y) | colvarmodule | [inline, static] |
print_total_forces_errning(bool warn_total_forces) | colvarmodule | |
proxy | colvarmodule | [static] |
rand_gaussian(void) | colvarmodule | [static] |
read_colvar(std::string const &name) | colvarmodule | |
read_config_file(char const *config_file_name) | colvarmodule | |
read_config_string(std::string const &conf) | colvarmodule | |
read_index_file(char const *filename) | colvarmodule | |
read_objects_state(std::istream &is) | colvarmodule | |
read_restart(std::istream &is) | colvarmodule | |
read_traj(char const *traj_filename, long traj_read_begin, long traj_read_end) | colvarmodule | |
real typedef | colvarmodule | |
register_named_atom_group(atom_group *ag) | colvarmodule | |
request_total_force() | colvarmodule | [static] |
reset() | colvarmodule | |
reset_index_groups() | colvarmodule | |
residue_id typedef | colvarmodule | |
restart_out_freq | colvarmodule | [static] |
restart_out_name | colvarmodule | |
restart_version() const | colvarmodule | [inline] |
restart_version_int | colvarmodule | [protected] |
restart_version_number() const | colvarmodule | [inline] |
restart_version_str | colvarmodule | [protected] |
run_tcl_script(std::string const &filename) | colvarmodule | |
scripted_forces() | colvarmodule | [inline, static] |
scripting_after_biases | colvarmodule | [static] |
set_error_bits(int code) | colvarmodule | [static] |
setup_input() | colvarmodule | |
setup_output() | colvarmodule | |
sin(real const &x) | colvarmodule | [inline, static] |
size() const | colvarmodule | |
sqrt(real const &x) | colvarmodule | [inline, static] |
state_file_prefix(char const *filename) | colvarmodule | [static] |
step_absolute() | colvarmodule | [inline, static] |
step_number typedef | colvarmodule | |
step_relative() | colvarmodule | [inline, static] |
time_dependent_biases() const | colvarmodule | |
to_str(char const *s) | colvarmodule | [static] |
to_str(std::string const &s) | colvarmodule | [static] |
to_str(bool x) | colvarmodule | [static] |
to_str(int const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(size_t const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(long int const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(step_number const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(real const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(rvector const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(quaternion const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(colvarvalue const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(vector1d< real > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(matrix2d< real > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< int > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< size_t > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< long int > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< real > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< rvector > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< quaternion > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< colvarvalue > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
to_str(std::vector< std::string > const &x, size_t width=0, size_t prec=0) | colvarmodule | [static] |
total_bias_energy | colvarmodule | |
unregister_named_atom_group(atom_group *ag) | colvarmodule | |
update_colvar_forces() | colvarmodule | |
update_engine_parameters() | colvarmodule | |
usage_ | colvarmodule | [protected] |
use_scripted_forces | colvarmodule | [static] |
variables() | colvarmodule | |
variables_active() | colvarmodule | |
variables_active_smp() | colvarmodule | |
variables_active_smp_items() | colvarmodule | |
version() const | colvarmodule | [inline] |
version_number() const | colvarmodule | [inline] |
wrap_string(std::string const &s, size_t nchars) | colvarmodule | [static] |
write_output_files() | colvarmodule | |
write_restart(std::ostream &os) | colvarmodule | |
write_restart_file(std::string const &out_name) | colvarmodule | |
write_restart_string(std::string &output) | colvarmodule | |
write_traj(std::ostream &os) | colvarmodule | |
write_traj_files() | colvarmodule | |
write_traj_label(std::ostream &os) | colvarmodule | |
xyz_reader_use_count | colvarmodule | [protected] |
~colvarmodule() | colvarmodule | |