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Update Colvars library to version 2018-10-16

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This commit is contained in:
Giacomo Fiorin
2018-11-02 17:45:20 -04:00
parent a66d4c7451
commit 85a5cab663
24 changed files with 800 additions and 376 deletions
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35
lib/colvars/colvarscript.cpp
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@ -82,6 +82,14 @@ int colvarscript::run(int objc, unsigned char *const objv[])
int error_code = COLVARS_OK;
// If command is found in map, execute it
std::string const cmd_key("cv_"+cmd);
if (comm_str_map.count(cmd_key) > 0) {
error_code |= (*(comm_fns[comm_str_map[cmd_key]]))(
reinterpret_cast<void *>(this), objc, objv);
return error_code;
}
if (cmd == "colvar") {
if (objc < 3) {
result = "Missing parameters\n" + help_string();
@ -295,11 +303,12 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
}
if (subcmd == "delete") {
size_t i;
for (i = 0; i < cv->biases.size(); i++) {
while (cv->biases.size() > 0) {
size_t i = cv->biases.size()-1;
cvm::log("Warning: before deleting colvar " + cv->name
+ ", deleting parent bias " + cv->biases[i]->name);
delete cv->biases[i];
}
cv->biases.clear();
// colvar destructor is tasked with the cleanup
delete cv;
// TODO this could be done by the destructors
@ -373,6 +382,23 @@ int colvarscript::proc_colvar(colvar *cv, int objc, unsigned char *const objv[])
return COLVARS_OK;
}
if (subcmd == "modifycvcs") {
if (objc < 4) {
result = "cvcflags: missing parameter: vector of strings";
return COLVARSCRIPT_ERROR;
}
std::vector<std::string> const confs(proxy->script_obj_to_str_vector(objv[3]));
cvm::increase_depth();
int res = cv->update_cvc_config(confs);
cvm::decrease_depth();
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);
}
@ -547,6 +573,8 @@ std::string colvarscript::help_string() const
Managing the Colvars module:\n\
configfile <file name> -- read configuration from a file\n\
config <string> -- read configuration from the given string\n\
getconfig -- get the module's configuration string\n\
resetindexgroups -- clear the index groups loaded so far\n\
reset -- delete all internal configuration\n\
delete -- delete this Colvars module instance\n\
version -- return version of Colvars code\n\
@ -579,6 +607,7 @@ Accessing collective variables:\n\
colvar <name> gettotalforce -- return total force of 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> modifycvcs <str> -- pass new config strings to each CVC\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\