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colvarscript.cpp
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Thu, May 30, 19:04
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Sat, Jun 1, 19:04 (2 d)
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rLAMMPS lammps
colvarscript.cpp
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// -*- c++ -*-
#include <cstdlib>
#include <stdlib.h>
#include <string.h>
#include "colvarscript.h"
colvarscript::colvarscript(colvarproxy *p)
: proxy(p),
colvars(p->colvars),
proxy_error(0)
{
}
/// Run method based on given arguments
int colvarscript::run(int argc, char const *argv[]) {
result = "";
if (cvm::debug()) {
cvm::log("Called script run with " + cvm::to_str(argc) + " args");
for (int i = 0; i < argc; i++) { cvm::log(argv[i]); }
}
if (argc < 2) {
result = help_string();
return COLVARSCRIPT_OK;
}
std::string cmd = argv[1];
if (cmd == "colvar") {
return proc_colvar(argc-1, &(argv[1]));
}
if (cmd == "bias") {
return proc_bias(argc-1, &(argv[1]));
}
if (cmd == "version") {
result = COLVARS_VERSION;
return COLVARSCRIPT_OK;
}
if (cmd == "reset") {
/// Delete every child object
colvars->reset();
return COLVARSCRIPT_OK;
}
if (cmd == "delete") {
colvars->reset();
// Note: the delete bit may be ignored by some backends
// it is mostly useful in VMD
colvars->set_error_bits(DELETE_COLVARS);
return COLVARSCRIPT_OK;
}
if (cmd == "update") {
colvars->calc();
return COLVARSCRIPT_OK;
}
if (cmd == "list") {
if (argc == 2) {
for (std::vector<colvar *>::iterator cvi = colvars->colvars.begin();
cvi != colvars->colvars.end();
++cvi) {
result += (cvi == colvars->colvars.begin() ? "" : " ") + (*cvi)->name;
}
return COLVARSCRIPT_OK;
} else if (argc == 3 && !strcmp(argv[2], "biases")) {
for (std::vector<colvarbias *>::iterator bi = colvars->biases.begin();
bi != colvars->biases.end();
++bi) {
result += (bi == colvars->biases.begin() ? "" : " ") + (*bi)->name;
}
return COLVARSCRIPT_OK;
} else {
result = "Wrong arguments to command \"list\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
/// Parse config from file
if (cmd == "configfile") {
if (argc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
if (colvars->read_config_file(argv[2]) == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
result = "Error parsing configuration file";
return COLVARSCRIPT_ERROR;
}
}
/// Parse config from string
if (cmd == "config") {
if (argc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string conf = argv[2];
if (colvars->read_config_string(conf) == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
result = "Error parsing configuration string";
return COLVARSCRIPT_ERROR;
}
}
/// Load an input state file
if (cmd == "load") {
if (argc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
proxy->input_prefix_str = argv[2];
if (colvars->setup_input() == COLVARS_OK) {
return COLVARSCRIPT_OK;
} else {
result = "Error loading state file";
return COLVARSCRIPT_ERROR;
}
}
/// Save to an output state file
if (cmd == "save") {
if (argc < 3) {
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
proxy->output_prefix_str = argv[2];
int error = 0;
error |= colvars->setup_output();
error |= colvars->write_output_files();
return error ? COLVARSCRIPT_ERROR : COLVARSCRIPT_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 COLVARSCRIPT_OK;
}
if (cmd == "printframe") {
std::ostringstream os;
colvars->write_traj(os);
result = os.str();
return COLVARSCRIPT_OK;
}
if (cmd == "frame") {
if (argc == 2) {
int f = proxy->frame();
if (f >= 0) {
result = cvm::to_str(f);
return COLVARSCRIPT_OK;
} else {
result = "Frame number is not available";
return COLVARSCRIPT_ERROR;
}
} else if (argc == 3) {
// Failure of this function does not trigger an error, but
// returns the plain result to let scripts detect available frames
long int f = proxy->frame(strtol(argv[2], NULL, 10));
colvars->it = proxy->frame();
result = cvm::to_str(f);
return COLVARSCRIPT_OK;
} else {
result = "Wrong arguments to command \"frame\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_colvar(int argc, char const *argv[]) {
if (argc < 3) {
result = "Missing parameters\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string name = argv[1];
colvar *cv = cvm::colvar_by_name(name);
if (cv == NULL) {
result = "Colvar not found: " + name;
return COLVARSCRIPT_ERROR;
}
std::string subcmd = argv[2];
if (subcmd == "value") {
result = (cv->value()).to_simple_string();
return COLVARSCRIPT_OK;
}
if (subcmd == "width") {
result = cvm::to_str(cv->width, 0, cvm::cv_prec);
return COLVARSCRIPT_OK;
}
if (subcmd == "type") {
result = cv->value().type_desc(cv->value().value_type);
return COLVARSCRIPT_OK;
}
if (subcmd == "update") {
cv->calc();
cv->update();
result = (cv->value()).to_simple_string();
return COLVARSCRIPT_OK;
}
if (subcmd == "delete") {
if (cv->biases.size() > 0) {
result = "Cannot delete a colvar currently used by biases, delete those biases first";
return COLVARSCRIPT_ERROR;
}
// 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 COLVARSCRIPT_OK;
}
if (subcmd == "getconfig") {
result = cv->get_config();
return COLVARSCRIPT_OK;
}
if (subcmd == "addforce") {
if (argc < 4) {
result = "addforce: missing parameter: force value\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string f_str = argv[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 COLVARSCRIPT_OK;
}
if (subcmd == "cvcflags") {
if (argc < 4) {
result = "cvcflags: missing parameter: vector of flags";
return COLVARSCRIPT_ERROR;
}
std::string flags_str = argv[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 COLVARSCRIPT_OK;
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_bias(int argc, char const *argv[]) {
if (argc < 3) {
result = "Missing parameters\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string name = argv[1];
colvarbias *b = cvm::bias_by_name(name);
if (b == NULL) {
result = "Bias not found: " + name;
return COLVARSCRIPT_ERROR;
}
std::string subcmd = argv[2];
if (subcmd == "energy") {
result = cvm::to_str(b->get_energy());
return COLVARSCRIPT_OK;
}
if (subcmd == "update") {
b->update();
result = cvm::to_str(b->get_energy());
return COLVARSCRIPT_OK;
}
if (subcmd == "getconfig") {
result = b->get_config();
return COLVARSCRIPT_OK;
}
// Subcommands for MW ABF
if (subcmd == "bin") {
int r = b->current_bin();
result = cvm::to_str(r);
return COLVARSCRIPT_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 COLVARSCRIPT_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 COLVARSCRIPT_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 COLVARSCRIPT_OK;
}
if (argc >= 4) {
std::string param = argv[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 COLVARSCRIPT_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\
update -- recalculate colvars and biases based\n\
printframe -- return a summary of the current frame\n\
printframelabels -- return labels to annotate printframe's output\n";
if (proxy->frame() != 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\
\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";
return buf;
}
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