Collective Variables Module - Developer Documentation
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colvarmodule Member List

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

acos(real const &x)colvarmoduleinlinestatic
analyze()colvarmodule
append_new_config(std::string const &conf)colvarmodule
asin(real const &x)colvarmoduleinlinestatic
atan2(real const &x, real const &y)colvarmoduleinlinestatic
atom_const_iter typedef (defined in colvarmodule)colvarmodule
atom_group_by_name(std::string const &name)colvarmodulestatic
atom_iter typedef (defined in colvarmodule)colvarmodule
atom_pos typedefcolvarmodule
backup_file(char const *filename)colvarmodulestatic
bias_by_name(std::string const &name)colvarmodulestatic
biasescolvarmodule
biases_active()colvarmodule
biases_active_colvarmoduleprivate
binary_restart (defined in colvarmodule)colvarmodule
calc()colvarmodule
calc_biases()colvarmodule
calc_colvars()colvarmodule
calc_scripted_forces()colvarmodule
catch_input_errors(int result)colvarmoduleprivate
change_configuration(std::string const &bias_name, std::string const &conf)colvarmodule
check_new_bias(std::string &conf, char const *key)colvarmoduleprivate
cite_feature(std::string const &feature)colvarmodule
clear_error() (defined in colvarmodule)colvarmodulestatic
close_traj_file()colvarmodule
colvar_by_name(std::string const &name)colvarmodulestatic
colvarmodule(colvarproxy *proxy)colvarmodule
colvarmodule()colvarmoduleprivate
colvarscolvarmoduleprivate
colvars_activecolvarmoduleprivate
colvars_smpcolvarmoduleprivate
colvars_smp_itemscolvarmoduleprivate
config_changed()colvarmodule
config_stringcolvarmoduleprivate
cos(real const &x)colvarmoduleinlinestatic
cv_preccolvarmodulestatic
cv_traj_freqcolvarmodulestatic
cv_traj_namecolvarmoduleprotected
cv_traj_write_labelscolvarmoduleprotected
cv_widthcolvarmodulestatic
cvm_output_prefixcolvarmoduleprivate
debug()colvarmoduleinlinestatic
debug_gradients_step_sizecolvarmodulestatic
decrease_depth()colvarmodulestatic
default_input_state_file_colvarmoduleprivate
depth()colvarmodulestatic
depth_scolvarmoduleprotected
depth_vcolvarmoduleprotected
dt()colvarmodulestatic
en_preccolvarmodulestatic
en_widthcolvarmodulestatic
end_of_step()colvarmodule
energy_difference(std::string const &bias_name, std::string const &conf)colvarmodule
error(std::string const &message, int code=-1)colvarmodulestatic
errorCodecolvarmoduleprivatestatic
exp(real const &x)colvarmoduleinlinestatic
extra_confcolvarmoduleprivate
fabs(real const &x)colvarmoduleinlinestatic
feature_report(int flag=0)colvarmodule
floor(real const &x)colvarmoduleinlinestatic
get_config() constcolvarmodule
get_error() (defined in colvarmodule)colvarmoduleinlinestatic
get_error_bit(int code) (defined in colvarmodule)colvarmodulestatic
getline(std::istream &is, std::string &line)colvarmodulestatic
increase_depth()colvarmodulestatic
index_file_namescolvarmodule
index_group_namescolvarmodule
index_groupscolvarmodule
input_state_buffer_colvarmoduleprivate
integer_power(real const &x, int const n)colvarmoduleinlinestatic
itcolvarmodulestatic
it_restartcolvarmodulestatic
it_widthcolvarmodulestatic
line_markercolvarmodulestatic
load_coords(char const *filename, std::vector< rvector > *pos, atom_group *atoms, std::string const &pdb_field, double pdb_field_value=0.0)colvarmodulestatic
load_coords_xyz(char const *filename, std::vector< rvector > *pos, atom_group *atoms, bool keep_open=false)colvarmodule
log(std::string const &message, int min_log_level=10)colvarmodulestatic
log_default_params()colvarmoduleinlinestatic
log_init_messages()colvarmoduleinlinestatic
log_input_files()colvarmoduleinlinestatic
log_level()colvarmoduleinlinestatic
log_level_colvarmoduleprivatestatic
log_output_files()colvarmoduleinlinestatic
log_user_params()colvarmoduleinlinestatic
logn(real const &x)colvarmoduleinlinestatic
main()colvarmodulestatic
named_atom_groupscolvarmoduleprivate
num_biases() constcolvarmodule
num_biases_feature(int feature_id) constcolvarmodule
num_biases_type(std::string const &type) constcolvarmodule
num_biases_types_used_colvarmoduleprivate
num_variables() constcolvarmodule
num_variables_feature(int feature_id) constcolvarmodule
open_traj_file(std::string const &file_name)colvarmodule
output_prefix()colvarmoduleinlinestatic
parsecolvarmoduleprotected
parse_biases(std::string const &conf)colvarmodule
parse_biases_type(std::string const &conf, char const *keyword)colvarmoduleprivate
parse_colvars(std::string const &conf)colvarmodule
parse_config(std::string &conf)colvarmodule
parse_global_params(std::string const &conf)colvarmodule
patch_version_intcolvarmoduleprivate
patch_version_number() constcolvarmoduleinline
position_distance(atom_pos const &pos1, atom_pos const &pos2)colvarmodulestatic
pow(real const &x, real const &y)colvarmoduleinlinestatic
print_total_forces_errning(bool warn_total_forces)colvarmodule
proxycolvarmodulestatic
rand_gaussian()colvarmodulestatic
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_objects_state(memory_stream &is)colvarmodule
read_state(std::istream &is)colvarmodule
read_state(memory_stream &is)colvarmodule
read_state_template_(IST &is) (defined in colvarmodule)colvarmoduleprivate
read_traj(char const *traj_filename, long traj_read_begin, long traj_read_end)colvarmodule
real typedefcolvarmodule
register_named_atom_group(atom_group *ag)colvarmodule
request_total_force()colvarmodulestatic
reset()colvarmodule
reset_index_groups()colvarmodule
residue_id typedefcolvarmodule
restart_out_freqcolvarmodulestatic
restart_out_namecolvarmodule
restart_version() constcolvarmoduleinline
restart_version_intcolvarmoduleprotected
restart_version_number() constcolvarmoduleinline
restart_version_strcolvarmoduleprotected
run_tcl_script(std::string const &filename)colvarmodule
scripted_forces() (defined in colvarmodule)colvarmoduleinlinestatic
scripting_after_biasescolvarmodulestatic
set_error_bits(int code) (defined in colvarmodule)colvarmodulestatic
set_initial_step(step_number it)colvarmodule
set_input_state_buffer(size_t n, unsigned char *buf)colvarmodule
set_input_state_buffer(std::vector< unsigned char > &buf)colvarmodule
setup_input()colvarmodule
setup_output()colvarmodule
sin(real const &x)colvarmoduleinlinestatic
size() constcolvarmodule
source_Tcl_scriptcolvarmoduleprivate
sqrt(real const &x)colvarmoduleinlinestatic
state_file_prefix(char const *filename)colvarmodulestatic
step_absolute()colvarmoduleinlinestatic
step_number typedefcolvarmodule
step_relative()colvarmoduleinlinestatic
time_dependent_biases() constcolvarmodule
to_str(char const *s)colvarmodulestatic
to_str(std::string const &s)colvarmodulestatic
to_str(bool x)colvarmodulestatic
to_str(int const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(size_t const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(long int const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(step_number const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(real const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(rvector const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(quaternion const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(colvarvalue const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(vector1d< real > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(matrix2d< real > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< int > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< size_t > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< long int > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< real > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< rvector > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< quaternion > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< colvarvalue > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
to_str(std::vector< std::string > const &x, size_t width=0, size_t prec=0)colvarmodulestatic
total_bias_energycolvarmodule
unregister_named_atom_group(atom_group *ag)colvarmodule
update_colvar_forces()colvarmodule
update_engine_parameters()colvarmodule
usage_colvarmoduleprotected
use_scripted_forcescolvarmodulestatic
variables()colvarmodule
variables_active()colvarmodule
variables_active_smp()colvarmodule
variables_active_smp_items()colvarmodule
version() constcolvarmoduleinline
version_intcolvarmoduleprivate
version_number() constcolvarmoduleinline
wrap_string(std::string const &s, size_t nchars)colvarmodulestatic
write_output_files()colvarmodule
write_restart_file(std::string const &out_name)colvarmodule
write_restart_string(std::string &output)colvarmodule
write_state(std::ostream &os)colvarmodule
write_state(memory_stream &os)colvarmodule
write_state_buffer(std::vector< unsigned char > &buffer)colvarmodule
write_state_template_(OST &os) (defined in colvarmodule)colvarmoduleprivate
write_traj(std::ostream &os)colvarmodule
write_traj_files()colvarmodule
write_traj_label(std::ostream &os)colvarmodule
xyz_reader_use_countcolvarmoduleprotected
~colvarmodule()colvarmodule