---

colvarscript_commands.h

Go to the documentation of this file.

// -*- 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.

#ifndef COLVARSCRIPT_COMMANDS_H
#define COLVARSCRIPT_COMMANDS_H

// The following is a complete definition of the scripting API.

// The CVSCRIPT macro is used in four distinct contexts:
// 1) Expand to the functions' prototypes (when included generically)
// 2) List colvarscript::command entries (when included in colvarscript.h)
// 3) Implement colvarscript::init() (when included in colvarscript.cpp)
// 4) Define the functions' bodies (when included in colvarscript_commands.cpp)


// Each command is created by an instance of the CVSCRIPT macro

// The arguments of the CVSCRIPT macro are:

// COMM = the id of the command (must be a member of colvarscript::command)

// HELP = short description (C string literal) for the command; the second line
//        is optional, and documents the return value (if any)

// N_ARGS_MIN = the lowest number of arguments allowed

// N_ARGS_MAX = the highest number of arguments allowed

// ARGS = multi-line string literal describing each parameter; each line
//        follows the format "name : type - description"

// FN_BODY = the implementation of the function; this should be a thin wrapper
//           over existing functions; the "script" pointer to the colvarscript
//           object is already set by the CVSCRIPT_COMM_FN macro; see also the
//           functions in colvarscript_commands.h.

#ifndef CVSCRIPT_COMM_FNAME
#define CVSCRIPT_COMM_FNAME(COMM) cvscript_ ## COMM
#endif

// If CVSCRIPT is not defined, this file yields the function prototypes
#ifndef CVSCRIPT

#ifdef __cplusplus
#define CVSCRIPT_COMM_PROTO(COMM)                                       \
  extern "C" int CVSCRIPT_COMM_FNAME(COMM)(void *,                      \
                                           int, unsigned char *const *);
#else
#define CVSCRIPT_COMM_PROTO(COMM)                                       \
  int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
#endif

#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY)  \
  CVSCRIPT_COMM_PROTO(COMM)


// Utility functions used to query the command database
extern "C" {

  int cvscript_n_commands();

  char const ** cvscript_command_names();

  char const *cvscript_command_help(char const *cmd);

  char const *cvscript_command_rethelp(char const *cmd);

  char const *cvscript_command_arghelp(char const *cmd, int i);

  char const *cvscript_command_full_help(char const *cmd);

  int cvscript_command_n_args_min(char const *cmd);

  int cvscript_command_n_args_max(char const *cmd);

}

#endif


CVSCRIPT(cv_addenergy,
         "Add an energy to the MD engine (no effect in VMD)",
         1, 1,
         "E : float - Amount of energy to add",
         char const *Earg =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         cvm::main()->total_bias_energy += strtod(Earg, NULL);
         return cvm::get_error(); // TODO Make this multi-language
         )

CVSCRIPT(cv_bias,
         "Prefix for bias-specific commands",
         0, 0,
         "",
         // This cannot be executed from a command line
         return COLVARS_OK;
         )

CVSCRIPT(cv_colvar,
         "Prefix for colvar-specific commands",
         0, 0,
         "",
         // This cannot be executed from a command line
         return COLVARS_OK;
         )

CVSCRIPT(cv_config,
         "Read configuration from the given string",
         1, 1,
         "conf : string - Configuration string",
         char const *conf_str =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         std::string const conf(conf_str);
         script->proxy()->add_config("config", conf);
         if (script->proxy()->engine_ready()) {
           // Engine allows immediate initialization
           if ((script->proxy()->parse_module_config() |
                script->proxy()->setup()) == COLVARS_OK) {
             return COLVARS_OK;
           } else {
             script->add_error_msg("Error parsing configuration string");
             return COLVARSCRIPT_ERROR;
           }
         }
         // Engine not ready, config will be read during proxy->setup()
         return COLVARS_OK;
         )

CVSCRIPT(cv_configfile,
         "Read configuration from a file",
         1, 1,
         "conf_file : string - Path to configuration file",
         char const *conf_file_name =
         script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         script->proxy()->add_config("configfile", std::string(conf_file_name));
         if (script->proxy()->engine_ready()) {
           // Engine allows immediate initialization
           if ((script->proxy()->parse_module_config() |
                script->proxy()->setup()) == COLVARS_OK) {
             return COLVARS_OK;
           } else {
             script->add_error_msg("Error parsing configuration file");
             return COLVARSCRIPT_ERROR;
           }
         }
         // Engine not ready, config will be read during proxy->setup()
         return COLVARS_OK;
         )

CVSCRIPT(cv_delete,
         "Delete this Colvars module instance (VMD only)",
         0, 0,
         "",
         return script->proxy()->request_deletion();
         )

CVSCRIPT(cv_featurereport,
         "Return a summary of Colvars features used so far and their citations\n"
         "report : string - Feature report and citations",
         0, 0,
         "",
         return script->set_result_str(script->module()->feature_report());
         )

CVSCRIPT(cv_frame,
         "Get or set current frame number (VMD only)\n"
         "frame : integer - Frame number",
         0, 1,
         "frame : integer - Frame number",
         char const *arg =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         if (arg == NULL) {
           long int f = -1;
           if (script->proxy()->get_frame(f) == COLVARS_OK) {
             script->set_result_long_int(f);
             return COLVARS_OK;
           } else {
             script->add_error_msg("Frame number is not available");
             return COLVARSCRIPT_ERROR;
           }
         } else {
           int const f = strtol(const_cast<char *>(arg), NULL, 10);
           int error_code = script->proxy()->set_frame(f);
           if (error_code == COLVARS_NO_SUCH_FRAME) {
             script->add_error_msg("Invalid frame number: \""+std::string(arg)+
                                   "\"\n");
           }
           return error_code;
         }
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatomappliedforces,
         "Get the list of forces applied by Colvars to atoms\n"
         "forces : array of arrays of floats - Atomic forces",
         0, 0,
         "",
         script->set_result_rvector_vec(*(script->proxy()->get_atom_applied_forces()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatomappliedforcesmax,
         "Get the maximum norm of forces applied by Colvars to atoms\n"
         "force : float - Maximum atomic force",
         0, 0,
         "",
         script->set_result_real(script->proxy()->max_atoms_applied_force());
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatomappliedforcesmaxid,
         "Get the atom ID with the largest applied force\n"
         "id : int - ID of the atom with the maximum atomic force",
         0, 0,
         "",
         script->set_result_int(script->proxy()->max_atoms_applied_force_id());
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatomappliedforcesrms,
         "Get the root-mean-square norm of forces applied by Colvars to atoms\n"
         "force : float - RMS atomic force",
         0, 0,
         "",
         script->set_result_real(script->proxy()->rms_atoms_applied_force());
         return COLVARS_OK;
         )

CVSCRIPT(cv_resetatomappliedforces,
         "Reset forces applied by Colvars to atoms",
         0, 0,
         "",
            size_t i;
            std::vector<cvm::rvector> *f = script->proxy()->modify_atom_applied_forces();
            for (i = 0; i < f->size(); i++) {
              (*f)[i].reset();
            }
            return COLVARS_OK;
         )

CVSCRIPT(cv_getatomids,
         "Get the list of indices of atoms used in Colvars\n"
         "indices : array of ints - Atom indices",
         0, 0,
         "",
         script->set_result_int_vec(*(script->proxy()->get_atom_ids()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatomcharges,
         "Get the list of charges of atoms used in Colvars\n"
         "charges : array of floats - Atomic charges",
         0, 0,
         "",
         script->set_result_real_vec(*(script->proxy()->get_atom_charges()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatommasses,
         "Get the list of masses of atoms used in Colvars\n"
         "masses : array of floats - Atomic masses",
         0, 0,
         "",
         script->set_result_real_vec(*(script->proxy()->get_atom_masses()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatompositions,
         "Get the list of cached positions of atoms used in Colvars\n"
         "positions : array of arrays of floats - Atomic positions",
         0, 0,
         "",
         script->set_result_rvector_vec(*(script->proxy()->get_atom_positions()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getatomtotalforces,
         "Get the list of cached total forces of atoms used in Colvars\n"
         "forces : array of arrays of floats - Atomic total foces",
         0, 0,
         "",
         script->set_result_rvector_vec(*(script->proxy()->get_atom_total_forces()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getconfig,
         "Get the module's configuration string read so far\n"
         "conf : string - Current configuration string",
         0, 0,
         "",
         script->set_result_str(cvm::main()->get_config());
         return COLVARS_OK;
         )

CVSCRIPT(cv_getenergy,
         "Get the current Colvars energy\n"
         "E : float - Amount of energy (internal units)",
         0, 0,
         "",
         script->set_result_real(cvm::main()->total_bias_energy);
         return COLVARS_OK;
         )

CVSCRIPT(cv_getnumactiveatomgroups,
         "Get the number of atom groups that currently have positive ref counts\n"
         "count : integer - Total number of atom groups",
         0, 0,
         "",
         script->set_result_int(static_cast<int>(script->proxy()->get_num_active_atom_groups()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getnumactiveatoms,
         "Get the number of atoms that currently have positive ref counts\n"
         "count : integer - Total number of atoms",
         0, 0,
         "",
         script->set_result_int(static_cast<int>(script->proxy()->get_num_active_atoms()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getnumatoms,
         "Get the number of requested atoms, including those not in use now\n"
         "count : integer - Total number of atoms",
         0, 0,
         "",
         script->set_result_int(static_cast<int>(script->proxy()->get_atom_ids()->size()));
         return COLVARS_OK;
         )

CVSCRIPT(cv_getstepabsolute,
         "Get the current step number of the simulation (including restarts)\n"
         "step : int - Absolute step number",
         0, 0,
         "",
         script->set_result_int(cvm::step_absolute());
         return COLVARS_OK;
         )

CVSCRIPT(cv_getsteprelative,
         "Get the current step number from the start of this job\n"
         "step : int - Relative step number",
         0, 0,
         "",
         script->set_result_int(cvm::step_relative());
         return COLVARS_OK;
         )

CVSCRIPT(cv_help,
         "Get the help string of the Colvars scripting interface\n"
         "help : string - Help string",
         0, 1,
         "command : string - Get the help string of this specific command",
         unsigned char *const cmdobj =
           script->get_module_cmd_arg(0, objc, objv);
         if (cmdobj) {
           std::string const cmdstr(script->obj_to_str(cmdobj));
           if (cmdstr.size()) {
             if (cmdstr == std::string("colvar")) {
               script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_colvar));
             } else if (cmdstr == std::string("bias")) {
               script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_bias));
             } else {
               script->set_result_str(script->get_command_cmdline_help(colvarscript::use_module,
                                                                       cmdstr));
             }
             return cvm::get_error();
           } else {
             return COLVARSCRIPT_ERROR;
           }
         } else {
           script->set_result_str(script->get_cmdline_help_summary(colvarscript::use_module));
           return COLVARS_OK;
         }
         )

CVSCRIPT(cv_languageversion,
         "Get the C++ language version number\n"
         "version : string - C++ language version",
         0, 0,
         "",
         script->set_result_int(__cplusplus);
         return COLVARS_OK;
         )

CVSCRIPT(cv_list,
         "Return a list of all variables or biases\n"
         "list : sequence of strings - List of elements",
         0, 1,
         "param : string - \"colvars\" or \"biases\"; default is \"colvars\"",
         std::string res;
         unsigned char *const kwarg = script->get_module_cmd_arg(0, objc, objv);
         std::string const kwstr = kwarg ? script->obj_to_str(kwarg) :
           std::string("colvars");
         if (kwstr == "colvars") {
           for (std::vector<colvar *>::iterator cvi = script->module()->variables()->begin();
                cvi != script->module()->variables()->end();
                ++cvi) {
             res += (cvi == script->module()->variables()->begin() ? "" : " ") + (*cvi)->name;
           }
           script->set_result_str(res);
           return COLVARS_OK;
         } else if (kwstr == "biases") {
           for (std::vector<colvarbias *>::iterator bi = script->module()->biases.begin();
                bi != script->module()->biases.end();
                ++bi) {
             res += (bi == script->module()->biases.begin() ? "" : " ") + (*bi)->name;
           }
           script->set_result_str(res);
           return COLVARS_OK;
         } else {
           script->add_error_msg("Wrong arguments to command \"list\"\n");
           return COLVARSCRIPT_ERROR;
         }
         )

CVSCRIPT(cv_listcommands,
         "Get the list of script functions, prefixed with \"cv_\", \"colvar_\" or \"bias_\"\n"
         "list : sequence of strings - List of commands",
         0, 0,
         "",
         int const n_commands = cvscript_n_commands();
         char const **command_names = cvscript_command_names();
         std::string result;
         for (int i = 0; i < n_commands; i++) {
           if (i > 0) result.append(1, ' ');
           result.append(std::string(command_names[i]));
         }
         script->set_result_str(result);
         return COLVARS_OK;
         )

CVSCRIPT(cv_listindexfiles,
         "Get a list of the index files loaded in this session",
         0, 0,
         "",
         int const n_files = script->module()->index_file_names.size();
         std::string result;
         for (int i = 0; i < n_files; i++) {
           if (i > 0) result.append(1, ' ');
           result.append(script->module()->index_file_names[i]);
         }
         script->set_result_str(result);
         return COLVARS_OK;
         )

CVSCRIPT(cv_load,
         "Load data from a state file into all matching colvars and biases",
         1, 1,
         "prefix : string - Path to existing state file or input prefix",
         char const *arg =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         script->proxy()->input_prefix() = cvm::state_file_prefix(arg);
         if (script->module()->setup_input() == COLVARS_OK) {
           return COLVARS_OK;
         } else {
           script->add_error_msg("Error loading state file");
           return COLVARSCRIPT_ERROR;
         }
         )

CVSCRIPT(cv_loadfromstring,
         "Load state data from a string into all matching colvars and biases",
         1, 1,
         "buffer : string - String buffer containing the state information",
         char const *arg =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         script->proxy()->input_buffer() = arg;
         if (script->module()->setup_input() == COLVARS_OK) {
           return COLVARS_OK;
         } else {
           script->add_error_msg("Error loading state string");
           return COLVARSCRIPT_ERROR;
         }
         )

CVSCRIPT(cv_molid,
         "Get or set the molecule ID on which Colvars is defined (VMD only)\n"
         "molid : integer - Current molecule ID",
         0, 1,
         "molid : integer - New molecule ID; -1 means undefined",
         char const *arg =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         if (arg == NULL) {
           int molid = -1;
           script->proxy()->get_molid(molid);
           script->set_result_int(molid);
           return COLVARS_OK;
         } else {
           script->add_error_msg("Error: To change the molecule ID in VMD, use cv delete first.");
           return COLVARS_NOT_IMPLEMENTED;
         }
         )

CVSCRIPT(cv_printframe,
         "Return the values that would be written to colvars.traj\n"
         "values : string - The values\n",
         0, 0,
         "",
         std::ostringstream os;
         script->module()->write_traj(os);
         script->set_result_str(os.str());
         return COLVARS_OK;
         )

CVSCRIPT(cv_printframelabels,
         "Return the labels that would be written to colvars.traj\n"
         "Labels : string - The labels",
         0, 0,
         "",
         std::ostringstream os;
         script->module()->write_traj_label(os);
         script->set_result_str(os.str());
         return COLVARS_OK;
         )

CVSCRIPT(cv_reset,
         "Delete all internal configuration",
         0, 0,
         "",
         return script->module()->reset();
         )

CVSCRIPT(cv_resetindexgroups,
         "Clear the index groups loaded so far, allowing to replace them",
         0, 0,
         "",
         cvm::main()->index_group_names.clear();
         cvm::main()->index_groups.clear();
         return COLVARS_OK;
         )

CVSCRIPT(cv_save,
         "Change the prefix of all output files and save them",
         1, 1,
         "prefix : string - Output prefix with trailing \".colvars.state\" gets removed)",
         std::string const prefix =
           cvm::state_file_prefix(script->obj_to_str(script->get_module_cmd_arg(0, objc, objv)));
         script->proxy()->output_prefix() = prefix;
         int error_code = COLVARS_OK;
         error_code |= script->module()->setup_output();
         error_code |= script->module()->write_restart_file(prefix+
                                                            ".colvars.state");
         error_code |= script->module()->write_output_files();
         return error_code;
         )

CVSCRIPT(cv_savetostring,
         "Write the Colvars state to a string and return it\n"
         "state : string - The saved state",
         0, 0,
         "",
         return script->module()->write_restart_string(script->modify_str_result());
         )

CVSCRIPT(cv_targettemperature,
         "Get/set target temperature, overriding what the MD engine provides\n"
         "T : float - Current target temperature in K",
         0, 1,
         "T : float - New target temperature in K",
         char const *Targ =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         if (Targ == NULL) {
           return script->set_result_real(script->proxy()->target_temperature());
         } else {
           return script->proxy()->set_target_temperature(strtod(Targ, NULL));
         }
         )

CVSCRIPT(cv_units,
         "Get or set the current Colvars unit system\n"
         "units : string - The current unit system",
         0, 1,
         "units : string - The new unit system",
         char const *argstr =
           script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
         if (argstr) {
           return cvm::proxy->set_unit_system(argstr, false);
         } else {
           script->set_result_str(cvm::proxy->units);
           return COLVARS_OK;
         }
         )

CVSCRIPT(cv_update,
         "Recalculate colvars and biases",
         0, 0,
         "",
         int error_code = script->proxy()->update_input();
         if (error_code) {
           script->add_error_msg("Error updating the Colvars module (input)");
           return error_code;
         }
         error_code |= script->module()->calc();
         if (error_code) {
           script->add_error_msg("Error updating the Colvars module (calc)");
           return error_code;
         }
         error_code |= script->proxy()->update_output();
         if (error_code) {
           script->add_error_msg("Error updating the Colvars module (output)");
         }
         return error_code;
         )

CVSCRIPT(cv_version,
         "Get the Colvars Module version string\n"
         "version : string - Colvars version",
         0, 0,
         "",
         script->set_result_str(COLVARS_VERSION);
         return COLVARS_OK;
         )

// This guard allows compiling colvar and bias function bodies in their
// respecitve files instead of colvarscript_commands.o
#ifndef COLVARSCRIPT_COMMANDS_GLOBAL
#include "colvarscript_commands_colvar.h"
#include "colvarscript_commands_bias.h"
#endif

#endif // #ifndef COLVARSCRIPT_COMMANDS_H

---