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colvarscript.cpp
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Wed, Jul 9, 05:22

colvarscript.cpp
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// -*- 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.
#include <cstdlib>
#include <stdlib.h>
#include <string.h>
#include "colvarscript.h"
#include "colvarproxy.h"
#include "colvardeps.h"
colvarscript::colvarscript(colvarproxy *p)
: proxy(p),
colvars(p->colvars),
proxy_error(0)
{
}
extern "C" {
// Generic hooks; NAMD and VMD have Tcl-specific versions in the respective proxies
int run_colvarscript_command(int objc, unsigned char *const objv[])
{
colvarproxy *cvp = cvm::proxy;
if (!cvp) {
return -1;
}
if (!cvp->script) {
cvm::error("Called run_colvarscript_command without a script object initialized.\n");
return -1;
}
return cvp->script->run(objc, objv);
}
const char * get_colvarscript_result()
{
colvarproxy *cvp = cvm::proxy;
if (!cvp->script) {
cvm::error("Called run_colvarscript_command without a script object initialized.\n");
return "";
}
return cvp->script->result.c_str();
}
}
/// Run method based on given arguments
int colvarscript::run(int objc, unsigned char *const objv[])
{
result.clear();
if (cvm::debug()) {
cvm::log("Called script run with " + cvm::to_str(objc) + " args:");
for (int i = 0; i < objc; i++) {
cvm::log(obj_to_str(objv[i]));
}
}
if (objc < 2) {
result = help_string();
return COLVARS_OK;
}
std::string const cmd(obj_to_str(objv[1]));
int error_code = COLVARS_OK;
if (cmd == "colvar") {
if (objc < 3) {
result = "Missing parameters\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string const name(obj_to_str(objv[2]));
colvar *cv = cvm::colvar_by_name(name);
if (cv == NULL) {
result = "Colvar not found: " + name;
return COLVARSCRIPT_ERROR;
}
return proc_colvar(cv, objc-1, &(objv[1]));
}
if (cmd == "bias") {
if (objc < 3) {
result = "Missing parameters\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string const name(obj_to_str(objv[2]));
colvarbias *b = cvm::bias_by_name(name);
if (b == NULL) {
result = "Bias not found: " + name;
return COLVARSCRIPT_ERROR;
}
return proc_bias(b, objc-1, &(objv[1]));
}
if (cmd == "version") {
result = COLVARS_VERSION;
return COLVARS_OK;
}
if (cmd == "reset") {
/// Delete every child object
colvars->reset();
return COLVARS_OK;
}
if (cmd == "delete") {
// Note: the delete bit may be ignored by some backends
// it is mostly useful in VMD
colvars->set_error_bits(DELETE_COLVARS);
return COLVARS_OK;
}
if (cmd == "update") {
error_code |= proxy->update_input();
error_code |= colvars->calc();
error_code |= proxy->update_output();
if (error_code) {
result += "Error updating the Colvars module.\n";
}
return error_code;
}
if (cmd == "list") {
if (objc == 2) {
for (std::vector<colvar *>::iterator cvi = colvars->colvars.begin();
cvi != colvars->colvars.end();
++cvi) {
result += (cvi == colvars->colvars.begin() ? "" : " ") + (*cvi)->name;
}
return COLVARS_OK;
} else if (objc == 3 && !strcmp(obj_to_str(objv[2]), "biases")) {
for (std::vector<colvarbias *>::iterator bi = colvars->biases.begin();
bi != colvars->biases.end();
++bi) {
result += (bi == colvars->biases.begin() ? "" : " ") + (*bi)->name;
}
return COLVARS_OK;
} else {
result = "Wrong arguments to command \"list\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
/// Parse config from file
if (cmd == "configfile") {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
if (colvars->read_config_file(obj_to_str(objv[2])) == COLVARS_OK) {
return COLVARS_OK;
} else {
result = "Error parsing configuration file";
return COLVARSCRIPT_ERROR;
}
}
/// Parse config from string
if (cmd == "config") {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string const conf(obj_to_str(objv[2]));
if (colvars->read_config_string(conf) == COLVARS_OK) {
return COLVARS_OK;
} else {
result = "Error parsing configuration string";
return COLVARSCRIPT_ERROR;
}
}
/// Load an input state file
if (cmd == "load") {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
proxy->input_prefix() = obj_to_str(objv[2]);
if (colvars->setup_input() == COLVARS_OK) {
return COLVARS_OK;
} else {
result = "Error loading state file";
return COLVARSCRIPT_ERROR;
}
}
/// Save to an output state file
if (cmd == "save") {
if (objc < 3) {
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
proxy->output_prefix() = obj_to_str(objv[2]);
int error = 0;
error |= colvars->setup_output();
error |= colvars->write_output_files();
return error ? COLVARSCRIPT_ERROR : COLVARS_OK;
}
/// Print the values that would go on colvars.traj
if (cmd == "printframelabels") {
std::ostringstream os;
colvars->write_traj_label(os);
result = os.str();
return COLVARS_OK;
}
if (cmd == "printframe") {
std::ostringstream os;
colvars->write_traj(os);
result = os.str();
return COLVARS_OK;
}
if (cmd == "frame") {
if (objc == 2) {
long int f;
int error = proxy->get_frame(f);
if (error == COLVARS_OK) {
result = cvm::to_str(f);
return COLVARS_OK;
} else {
result = "Frame number is not available";
return COLVARSCRIPT_ERROR;
}
} else if (objc == 3) {
// Failure of this function does not trigger an error, but
// returns nonzero, to let scripts detect available frames
int error = proxy->set_frame(strtol(obj_to_str(objv[2]), NULL, 10));
result = cvm::to_str(error == COLVARS_OK ? 0 : -1);
return COLVARS_OK;
} else {
result = "Wrong arguments to command \"frame\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
if (cmd == "addenergy") {
if (objc == 3) {
colvars->total_bias_energy += strtod(obj_to_str(objv[2]), NULL);
return COLVARS_OK;
} else {
result = "Wrong arguments to command \"addenergy\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) {
std::string const subcmd(obj_to_str(objv[2]));
if (subcmd == "value") {
result = (cv->value()).to_simple_string();
return COLVARS_OK;
}
if (subcmd == "width") {
result = cvm::to_str(cv->width, 0, cvm::cv_prec);
return COLVARS_OK;
}
if (subcmd == "type") {
result = cv->value().type_desc(cv->value().value_type);
return COLVARS_OK;
}
if (subcmd == "update") {
cv->calc();
cv->update_forces_energy();
result = (cv->value()).to_simple_string();
return COLVARS_OK;
}
if (subcmd == "delete") {
size_t i;
for (i = 0; i < cv->biases.size(); i++) {
delete cv->biases[i];
}
cv->biases.clear();
// colvar destructor is tasked with the cleanup
delete cv;
// TODO this could be done by the destructors
colvars->write_traj_label(*(colvars->cv_traj_os));
return COLVARS_OK;
}
if (subcmd == "getconfig") {
result = cv->get_config();
return COLVARS_OK;
}
if (subcmd == "getappliedforce") {
result = (cv->applied_force()).to_simple_string();
return COLVARS_OK;
}
if (subcmd == "getsystemforce") {
// TODO warning here
result = (cv->total_force()).to_simple_string();
return COLVARS_OK;
}
if (subcmd == "gettotalforce") {
result = (cv->total_force()).to_simple_string();
return COLVARS_OK;
}
if (subcmd == "addforce") {
if (objc < 4) {
result = "addforce: missing parameter: force value\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string const f_str(obj_to_str(objv[3]));
std::istringstream is(f_str);
is.width(cvm::cv_width);
is.precision(cvm::cv_prec);
colvarvalue force(cv->value());
force.is_derivative();
if (force.from_simple_string(is.str()) != COLVARS_OK) {
result = "addforce : error parsing force value";
return COLVARSCRIPT_ERROR;
}
cv->add_bias_force(force);
result = force.to_simple_string();
return COLVARS_OK;
}
if (subcmd == "cvcflags") {
if (objc < 4) {
result = "cvcflags: missing parameter: vector of flags";
return COLVARSCRIPT_ERROR;
}
std::string const flags_str(obj_to_str(objv[3]));
std::istringstream is(flags_str);
std::vector<bool> flags;
int flag;
while (is >> flag) {
flags.push_back(flag != 0);
}
int res = cv->set_cvc_flags(flags);
if (res != COLVARS_OK) {
result = "Error setting CVC flags";
return COLVARSCRIPT_ERROR;
}
result = "0";
return COLVARS_OK;
}
if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
return proc_features(cv, objc, objv);
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]) {
std::string const key(obj_to_str(objv[0]));
std::string const subcmd(obj_to_str(objv[2]));
if (subcmd == "energy") {
result = cvm::to_str(b->get_energy());
return COLVARS_OK;
}
if (subcmd == "update") {
b->update();
result = cvm::to_str(b->get_energy());
return COLVARS_OK;
}
if (subcmd == "getconfig") {
result = b->get_config();
return COLVARS_OK;
}
// Subcommands for MW ABF
if (subcmd == "bin") {
int r = b->current_bin();
result = cvm::to_str(r);
return COLVARS_OK;
}
if (subcmd == "binnum") {
int r = b->bin_num();
if (r < 0) {
result = "Error: calling bin_num() for bias " + b->name;
return COLVARSCRIPT_ERROR;
}
result = cvm::to_str(r);
return COLVARS_OK;
}
if (subcmd == "share") {
int r = b->replica_share();
if (r < 0) {
result = "Error: calling replica_share() for bias " + b->name;
return COLVARSCRIPT_ERROR;
}
result = cvm::to_str(r);
return COLVARS_OK;
}
// End commands for MW ABF
if (subcmd == "delete") {
// the bias destructor takes care of the cleanup at cvm level
delete b;
// TODO this could be done by the destructors
colvars->write_traj_label(*(colvars->cv_traj_os));
return COLVARS_OK;
}
if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
return proc_features(b, objc, objv);
}
if (objc >= 4) {
std::string const param(obj_to_str(objv[3]));
if (subcmd == "count") {
int index;
if (!(std::istringstream(param) >> index)) {
result = "bin_count: error parsing bin index";
return COLVARSCRIPT_ERROR;
}
result = cvm::to_str(b->bin_count(index));
return COLVARS_OK;
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_features(colvardeps *obj,
int objc, unsigned char *const objv[]) {
// size was already checked before calling
std::string const subcmd(obj_to_str(objv[2]));
if (objc == 3) {
if (subcmd == "state") {
// TODO make this returned as result?
obj->print_state();
return COLVARS_OK;
}
// get and set commands require more arguments
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
if ((subcmd == "get") || (subcmd == "set")) {
std::vector<colvardeps::feature *> const &features = obj->features();
std::string const req_feature(obj_to_str(objv[3]));
colvardeps::feature *f = NULL;
int fid = 0;
for (fid = 0; fid < int(features.size()); fid++) {
if (features[fid]->description ==
colvarparse::to_lower_cppstr(req_feature)) {
f = features[fid];
break;
}
}
if (f == NULL) {
result = "Error: feature \""+req_feature+"\" does not exist.\n";
return COLVARSCRIPT_ERROR;
} else {
if (! obj->is_available(fid)) {
result = "Error: feature \""+req_feature+"\" is unavailable.\n";
return COLVARSCRIPT_ERROR;
}
if (subcmd == "get") {
result = cvm::to_str(obj->is_enabled(fid) ? 1 : 0);
return COLVARS_OK;
}
if (subcmd == "set") {
if (objc == 5) {
std::string const yesno =
colvarparse::to_lower_cppstr(std::string(obj_to_str(objv[4])));
if ((yesno == std::string("yes")) ||
(yesno == std::string("on")) ||
(yesno == std::string("1"))) {
obj->enable(fid);
return COLVARS_OK;
} else if ((yesno == std::string("no")) ||
(yesno == std::string("off")) ||
(yesno == std::string("0"))) {
obj->disable(fid);
return COLVARS_OK;
}
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string colvarscript::help_string()
{
std::string buf;
buf = "Usage: cv <subcommand> [args...]\n\
\n\
Managing the Colvars module:\n\
configfile <file name> -- read configuration from a file\n\
config <string> -- read configuration from the given string\n\
reset -- delete all internal configuration\n\
delete -- delete this Colvars module instance\n\
version -- return version of colvars code\n\
\n\
Input and output:\n\
list -- return a list of all variables\n\
list biases -- return a list of all biases\n\
load <file name> -- load a state file (requires configuration)\n\
save <file name> -- save a state file (requires configuration)\n\
update -- recalculate colvars and biases\n\
addenergy <E> -- add <E> to the total bias energy\n\
printframe -- return a summary of the current frame\n\
printframelabels -- return labels to annotate printframe's output\n";
long int tmp;
if (proxy->get_frame(tmp) != COLVARS_NOT_IMPLEMENTED) {
buf += "\
frame -- return current frame number\n\
frame <new_frame> -- set frame number\n";
}
buf += "\n\
Accessing collective variables:\n\
colvar <name> value -- return the current value of colvar <name>\n\
colvar <name> update -- recalculate colvar <name>\n\
colvar <name> type -- return the type of colvar <name>\n\
colvar <name> delete -- delete colvar <name>\n\
colvar <name> addforce <F> -- apply given force on colvar <name>\n\
colvar <name> getconfig -- return config string of colvar <name>\n\
colvar <name> cvcflags <fl> -- enable or disable cvcs according to 0/1 flags\n\
colvar <name> get <f> -- get the value of the colvar feature <f>\n\
colvar <name> set <f> <val> -- set the value of the colvar feature <f>\n\
\n\
Accessing biases:\n\
bias <name> energy -- return the current energy of bias <name>\n\
bias <name> update -- recalculate bias <name>\n\
bias <name> delete -- delete bias <name>\n\
bias <name> getconfig -- return config string of bias <name>\n\
bias <name> get <f> -- get the value of the bias feature <f>\n\
bias <name> set <f> <val> -- set the value of the bias feature <f>\n\
";
return buf;
}

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