261 lines
8.9 KiB
C++
261 lines
8.9 KiB
C++
// -*- c++ -*-
|
|
|
|
// This file is part of the Collective Variables module (Colvars).
|
|
// The original version of Colvars and its updates are located at:
|
|
// https://github.com/Colvars/colvars
|
|
// Please update all Colvars source files before making any changes.
|
|
// If you wish to distribute your changes, please submit them to the
|
|
// Colvars repository at GitHub.
|
|
|
|
|
|
CVSCRIPT(colvar_addforce,
|
|
"Apply the given force onto this colvar (no effects outside run)\n"
|
|
"force : float or array - Applied force; matches colvar dimensionality",
|
|
1, 1,
|
|
"force : float or array - Applied force; must match colvar dimensionality",
|
|
std::string const f_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv)));
|
|
std::istringstream is(f_str);
|
|
is.width(cvm::cv_width);
|
|
is.precision(cvm::cv_prec);
|
|
colvarvalue force(this_colvar->value());
|
|
force.is_derivative();
|
|
if (force.from_simple_string(is.str()) != COLVARS_OK) {
|
|
script->add_error_msg("addforce : error parsing force value");
|
|
return COLVARSCRIPT_ERROR;
|
|
}
|
|
this_colvar->add_bias_force(force);
|
|
script->set_result_colvarvalue(force);
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_communicateforces,
|
|
"Communicate bias forces from this colvar to atoms",
|
|
0, 0,
|
|
"",
|
|
this_colvar->communicate_forces();
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_cvcflags,
|
|
"Enable or disable individual components by setting their active flags",
|
|
1, 1,
|
|
"flags : integer array - Zero/nonzero value disables/enables the CVC",
|
|
std::string const flags_str(script->obj_to_str(script->get_colvar_cmd_arg(0, objc, objv)));
|
|
std::istringstream is(flags_str);
|
|
std::vector<bool> flags;
|
|
int flag;
|
|
while (is >> flag) {
|
|
flags.push_back(flag != 0);
|
|
}
|
|
int res = this_colvar->set_cvc_flags(flags);
|
|
if (res != COLVARS_OK) {
|
|
script->add_error_msg("Error setting CVC flags");
|
|
return COLVARSCRIPT_ERROR;
|
|
}
|
|
script->set_result_str("0");
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_delete,
|
|
"Delete this colvar, along with all biases that depend on it",
|
|
0, 0,
|
|
"",
|
|
delete this_colvar;
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_get,
|
|
"Get the value of the given feature for this colvar\n"
|
|
"state : 1/0 - State of the given feature",
|
|
1, 1,
|
|
"feature : string - Name of the feature",
|
|
return script->proc_features(this_colvar, objc, objv);
|
|
)
|
|
|
|
CVSCRIPT(colvar_getappliedforce,
|
|
"Return the total of the forces applied to this colvar\n"
|
|
"force : float - Applied force; matches the colvar dimensionality",
|
|
0, 0,
|
|
"",
|
|
script->set_result_colvarvalue(this_colvar->applied_force());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_resetbiasforce,
|
|
"Return the total of the forces applied to this colvar",
|
|
0, 0,
|
|
"",
|
|
this_colvar->reset_bias_force();
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_getatomgroups,
|
|
"Return the atom indices used by this colvar as a list of lists\n"
|
|
"groups : array of arrays of ints - Atom indices",
|
|
0, 0,
|
|
"",
|
|
std::string result;
|
|
std::vector<std::vector<int> > lists = this_colvar->get_atom_lists();
|
|
std::vector<std::vector<int> >::iterator li = lists.begin();
|
|
for ( ; li != lists.end(); ++li) {
|
|
result += "{";
|
|
std::vector<int>::iterator lj = (*li).begin();
|
|
for ( ; lj != (*li).end(); ++lj) {
|
|
result += cvm::to_str(*lj);
|
|
result += " ";
|
|
}
|
|
result += "} ";
|
|
}
|
|
script->set_result_str(result);
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_getatomids,
|
|
"Return the list of atom indices used by this colvar\n"
|
|
"indices : array of ints - Atom indices",
|
|
0, 0,
|
|
"",
|
|
script->set_result_int_vec(this_colvar->atom_ids);
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_getconfig,
|
|
"Return the configuration string of this colvar\n"
|
|
"conf : string - Current configuration string",
|
|
0, 0,
|
|
"",
|
|
script->set_result_str(this_colvar->get_config());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_getgradients,
|
|
"Return the atomic gradients of this colvar\n"
|
|
"gradients : array of arrays of floats - Atomic gradients",
|
|
0, 0,
|
|
"",
|
|
script->set_result_rvector_vec(this_colvar->atomic_gradients);
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_gettotalforce,
|
|
"Return the sum of internal and external forces to this colvar\n"
|
|
"force : float - Total force; matches the colvar dimensionality",
|
|
0, 0,
|
|
"",
|
|
script->set_result_colvarvalue(this_colvar->total_force());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_getvolmapids,
|
|
"Return the list of volumetric map indices used by this colvar",
|
|
0, 0,
|
|
"",
|
|
script->set_result_int_vec(this_colvar->get_volmap_ids());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_help,
|
|
"Get a help summary or the help string of one colvar subcommand\n"
|
|
"help : string - Help string",
|
|
0, 1,
|
|
"command : string - Get the help string of this specific command",
|
|
unsigned char *const cmdobj =
|
|
script->get_colvar_cmd_arg(0, objc, objv);
|
|
if (this_colvar) {
|
|
}
|
|
if (cmdobj) {
|
|
std::string const cmdstr(script->obj_to_str(cmdobj));
|
|
if (cmdstr.size()) {
|
|
script->set_result_str(script->get_command_cmdline_help(colvarscript::use_colvar,
|
|
cmdstr));
|
|
return cvm::get_error();
|
|
} else {
|
|
return COLVARSCRIPT_ERROR;
|
|
}
|
|
} else {
|
|
script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_colvar));
|
|
return COLVARS_OK;
|
|
}
|
|
)
|
|
|
|
CVSCRIPT(colvar_modifycvcs,
|
|
"Modify configuration of individual components by passing string arguments",
|
|
1, 1,
|
|
"confs : sequence of strings - New configurations; empty strings are skipped",
|
|
std::vector<std::string> const confs(script->obj_to_str_vector(script->get_colvar_cmd_arg(0, objc, objv)));
|
|
cvm::increase_depth();
|
|
int res = this_colvar->update_cvc_config(confs);
|
|
cvm::decrease_depth();
|
|
if (res != COLVARS_OK) {
|
|
script->add_error_msg("Error setting CVC flags");
|
|
return COLVARSCRIPT_ERROR;
|
|
}
|
|
script->set_result_str("0");
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_run_ave,
|
|
"Get the current running average of the value of this colvar\n"
|
|
"value : float or array - Averaged value; matches the colvar dimensionality",
|
|
0, 0,
|
|
"",
|
|
script->set_result_colvarvalue(this_colvar->run_ave());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_set,
|
|
"Set the given feature of this colvar to a new value",
|
|
2, 2,
|
|
"feature : string - Name of the feature\n"
|
|
"value : string - String representation of the new feature value",
|
|
return script->proc_features(this_colvar, objc, objv);
|
|
)
|
|
|
|
CVSCRIPT(colvar_state,
|
|
"Print a string representation of the feature state of this colvar\n"
|
|
"state : string - The feature state",
|
|
0, 0,
|
|
"",
|
|
this_colvar->print_state();
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_type,
|
|
"Get the type description of this colvar\n"
|
|
"type : string - Type description",
|
|
0, 0,
|
|
"",
|
|
script->set_result_str(this_colvar->value().type_desc(this_colvar->value().value_type));
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_update,
|
|
"Recompute this colvar and return its up-to-date value\n"
|
|
"value : float or array - Current value; matches the colvar dimensionality",
|
|
0, 0,
|
|
"",
|
|
this_colvar->calc();
|
|
this_colvar->update_forces_energy();
|
|
script->set_result_colvarvalue(this_colvar->value());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_value,
|
|
"Get the current value of this colvar\n"
|
|
"value : float or array - Current value; matches the colvar dimensionality",
|
|
0, 0,
|
|
"",
|
|
script->set_result_colvarvalue(this_colvar->value());
|
|
return COLVARS_OK;
|
|
)
|
|
|
|
CVSCRIPT(colvar_width,
|
|
"Get the width of this colvar\n"
|
|
"width : float - Value of the width",
|
|
0, 0,
|
|
"",
|
|
script->set_result_str(cvm::to_str(this_colvar->width, 0,
|
|
cvm::cv_prec));
|
|
return COLVARS_OK;
|
|
)
|