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Update Colvars to version 2017-07-15 and support automated builds for it

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This commit is contained in:
Giacomo Fiorin
2017-07-19 14:10:43 -04:00
parent cc9b3864bf
commit ee6cac826e
52 changed files with 3473 additions and 2413 deletions
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150
lib/colvars/colvarscript.cpp
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@ -12,6 +12,7 @@
#include <string.h>
#include "colvarscript.h"
#include "colvarproxy.h"
#include "colvardeps.h"
@ -27,7 +28,7 @@ extern "C" {
// Generic hooks; NAMD and VMD have Tcl-specific versions in the respective proxies
int run_colvarscript_command(int argc, const char **argv)
int run_colvarscript_command(int objc, unsigned char *const objv[])
{
colvarproxy *cvp = cvm::proxy;
if (!cvp) {
@ -37,7 +38,7 @@ extern "C" {
cvm::error("Called run_colvarscript_command without a script object initialized.\n");
return -1;
}
return cvp->script->run(argc, argv);
return cvp->script->run(objc, objv);
}
const char * get_colvarscript_result()
@ -53,30 +54,52 @@ extern "C" {
/// Run method based on given arguments
int colvarscript::run(int argc, char const *argv[]) {
result = "";
int colvarscript::run(int objc, unsigned char *const objv[])
{
result.clear();
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]); }
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 (argc < 2) {
if (objc < 2) {
result = help_string();
return COLVARS_OK;
}
std::string cmd = argv[1];
std::string const cmd(obj_to_str(objv[1]));
int error_code = COLVARS_OK;
if (cmd == "colvar") {
return proc_colvar(argc-1, &(argv[1]));
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") {
return proc_bias(argc-1, &(argv[1]));
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") {
@ -102,20 +125,20 @@ int colvarscript::run(int argc, char const *argv[]) {
error_code |= colvars->calc();
error_code |= proxy->update_output();
if (error_code) {
result += "Error updating the colvars module.\n";
result += "Error updating the Colvars module.\n";
}
return error_code;
}
if (cmd == "list") {
if (argc == 2) {
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 (argc == 3 && !strcmp(argv[2], "biases")) {
} 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) {
@ -130,11 +153,11 @@ int colvarscript::run(int argc, char const *argv[]) {
/// Parse config from file
if (cmd == "configfile") {
if (argc < 3) {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
if (colvars->read_config_file(argv[2]) == COLVARS_OK) {
if (colvars->read_config_file(obj_to_str(objv[2])) == COLVARS_OK) {
return COLVARS_OK;
} else {
result = "Error parsing configuration file";
@ -144,11 +167,11 @@ int colvarscript::run(int argc, char const *argv[]) {
/// Parse config from string
if (cmd == "config") {
if (argc < 3) {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string conf = argv[2];
std::string const conf(obj_to_str(objv[2]));
if (colvars->read_config_string(conf) == COLVARS_OK) {
return COLVARS_OK;
} else {
@ -159,11 +182,11 @@ int colvarscript::run(int argc, char const *argv[]) {
/// Load an input state file
if (cmd == "load") {
if (argc < 3) {
if (objc < 3) {
result = "Missing arguments\n" + help_string();
return COLVARSCRIPT_ERROR;
}
proxy->input_prefix() = argv[2];
proxy->input_prefix() = obj_to_str(objv[2]);
if (colvars->setup_input() == COLVARS_OK) {
return COLVARS_OK;
} else {
@ -174,11 +197,11 @@ int colvarscript::run(int argc, char const *argv[]) {
/// Save to an output state file
if (cmd == "save") {
if (argc < 3) {
if (objc < 3) {
result = "Missing arguments";
return COLVARSCRIPT_ERROR;
}
proxy->output_prefix_str = argv[2];
proxy->output_prefix() = obj_to_str(objv[2]);
int error = 0;
error |= colvars->setup_output();
error |= colvars->write_output_files();
@ -200,7 +223,7 @@ int colvarscript::run(int argc, char const *argv[]) {
}
if (cmd == "frame") {
if (argc == 2) {
if (objc == 2) {
long int f;
int error = proxy->get_frame(f);
if (error == COLVARS_OK) {
@ -210,10 +233,10 @@ int colvarscript::run(int argc, char const *argv[]) {
result = "Frame number is not available";
return COLVARSCRIPT_ERROR;
}
} else if (argc == 3) {
} 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(argv[2], NULL, 10));
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 {
@ -223,8 +246,8 @@ int colvarscript::run(int argc, char const *argv[]) {
}
if (cmd == "addenergy") {
if (argc == 3) {
colvars->total_bias_energy += strtod(argv[2], NULL);
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();
@ -237,19 +260,9 @@ int colvarscript::run(int argc, char const *argv[]) {
}
int colvarscript::proc_colvar(int argc, char const *argv[]) {
if (argc < 3) {
result = "Missing parameters\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[]) {
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];
std::string const subcmd(obj_to_str(objv[2]));
if (subcmd == "value") {
result = (cv->value()).to_simple_string();
@ -278,11 +291,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
for (i = 0; i < cv->biases.size(); i++) {
delete cv->biases[i];
}
cv->biases.resize(0);
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);
colvars->write_traj_label(*(colvars->cv_traj_os));
return COLVARS_OK;
}
@ -308,11 +321,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
}
if (subcmd == "addforce") {
if (argc < 4) {
if (objc < 4) {
result = "addforce: missing parameter: force value\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string f_str = argv[3];
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);
@ -328,11 +341,11 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
}
if (subcmd == "cvcflags") {
if (argc < 4) {
if (objc < 4) {
result = "cvcflags: missing parameter: vector of flags";
return COLVARSCRIPT_ERROR;
}
std::string flags_str = argv[3];
std::string const flags_str(obj_to_str(objv[3]));
std::istringstream is(flags_str);
std::vector<bool> flags;
@ -351,7 +364,7 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
}
if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
return proc_features(cv, argc, argv);
return proc_features(cv, objc, objv);
}
result = "Syntax error\n" + help_string();
@ -359,20 +372,10 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
}
int colvarscript::proc_bias(int argc, char const *argv[]) {
if (argc < 3) {
result = "Missing parameters\n" + help_string();
return COLVARSCRIPT_ERROR;
}
int colvarscript::proc_bias(colvarbias *b, int objc, unsigned char *const objv[]) {
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];
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());
@ -422,16 +425,16 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
// 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);
colvars->write_traj_label(*(colvars->cv_traj_os));
return COLVARS_OK;
}
if ((subcmd == "get") || (subcmd == "set") || (subcmd == "state")) {
return proc_features(b, argc, argv);
return proc_features(b, objc, objv);
}
if (argc >= 4) {
std::string param = argv[3];
if (objc >= 4) {
std::string const param(obj_to_str(objv[3]));
if (subcmd == "count") {
int index;
if (!(std::istringstream(param) >> index)) {
@ -452,11 +455,11 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
int colvarscript::proc_features(colvardeps *obj,
int argc, char const *argv[]) {
int objc, unsigned char *const objv[]) {
// size was already checked before calling
std::string subcmd = argv[2];
std::string const subcmd(obj_to_str(objv[2]));
if (argc == 3) {
if (objc == 3) {
if (subcmd == "state") {
// TODO make this returned as result?
obj->print_state();
@ -470,7 +473,7 @@ int colvarscript::proc_features(colvardeps *obj,
if ((subcmd == "get") || (subcmd == "set")) {
std::vector<colvardeps::feature *> &features = obj->features();
std::string const req_feature(argv[3]);
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++) {
@ -499,9 +502,9 @@ int colvarscript::proc_features(colvardeps *obj,
}
if (subcmd == "set") {
if (argc == 5) {
if (objc == 5) {
std::string const yesno =
colvarparse::to_lower_cppstr(std::string(argv[4]));
colvarparse::to_lower_cppstr(std::string(obj_to_str(objv[4])));
if ((yesno == std::string("yes")) ||
(yesno == std::string("on")) ||
(yesno == std::string("1"))) {
@ -510,10 +513,7 @@ int colvarscript::proc_features(colvardeps *obj,
} else if ((yesno == std::string("no")) ||
(yesno == std::string("off")) ||
(yesno == std::string("0"))) {
// TODO disable() function does not exist yet,
// dependencies will not be resolved
// obj->disable(fid);
obj->set_enabled(fid, false);
obj->disable(fid);
return COLVARS_OK;
}
}
@ -533,11 +533,11 @@ std::string colvarscript::help_string()
std::string buf;
buf = "Usage: cv <subcommand> [args...]\n\
\n\
Managing the colvars module:\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\
delete -- delete this Colvars module instance\n\
version -- return version of colvars code\n\
\n\
Input and output:\n\