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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13396 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-04-06 15:14:53 +00:00
parent 2729e19d4a
commit 974e1eb022
4 changed files with 89 additions and 65 deletions
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21
lib/colvars/colvarmodule.cpp
View File

@ -598,7 +598,7 @@ int colvarmodule::calc() {
write_traj(cv_traj_os);
}
if (restart_out_freq) {
if (restart_out_freq && cv_traj_os.is_open()) {
// flush the trajectory file if we are at the restart frequency
if ( (cvm::step_relative() > 0) &&
((cvm::step_absolute() % restart_out_freq) == 0) ) {
@ -683,8 +683,10 @@ int colvarmodule::reset()
index_groups.clear();
index_group_names.clear();
// Do not close file here, as we might not be done with it yet.
cv_traj_os.flush();
if (cv_traj_os.is_open()) {
// Do not close file here, as we might not be done with it yet.
cv_traj_os.flush();
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -826,8 +828,11 @@ int colvarmodule::write_output_files()
}
cvm::decrease_depth();
// do not close to avoid problems with multiple NAMD runs
cv_traj_os.flush();
if (cv_traj_os.is_open()) {
// do not close to avoid problems with multiple NAMD runs
cv_traj_os.flush();
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
@ -985,8 +990,9 @@ std::ostream & colvarmodule::write_traj_label(std::ostream &os)
(*bi)->write_traj_label(os);
}
os << "\n";
if (cvm::debug())
if (cvm::debug()) {
os.flush();
}
cvm::decrease_depth();
return os;
}
@ -1010,8 +1016,9 @@ std::ostream & colvarmodule::write_traj(std::ostream &os)
(*bi)->write_traj(os);
}
os << "\n";
if (cvm::debug())
if (cvm::debug()) {
os.flush();
}
cvm::decrease_depth();
return os;
}

2
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2015-02-27"
#define COLVARS_VERSION "2015-03-15"
#endif
#ifndef COLVARS_DEBUG

127
lib/colvars/colvarscript.cpp
View File

@ -25,45 +25,7 @@ int colvarscript::run(int argc, char const *argv[]) {
}
if (argc < 2) {
result = "usage: "+std::string(argv[0])+" <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) {
result += "\
frame -- return current frame number\n\
frame <new_frame> -- set frame number\n";
}
result += "\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\
\n\
";
result = help_string();
return COLVARSCRIPT_OK;
}
@ -117,7 +79,7 @@ Accessing biases:\n\
}
return COLVARSCRIPT_OK;
} else {
result = "Wrong arguments to command \"list\"";
result = "Wrong arguments to command \"list\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
@ -125,12 +87,13 @@ Accessing biases:\n\
/// Parse config from file
if (cmd == "configfile") {
if (argc < 3) {
result = "Missing arguments";
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;
}
}
@ -138,13 +101,14 @@ Accessing biases:\n\
/// Parse config from string
if (cmd == "config") {
if (argc < 3) {
result = "Missing arguments";
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;
}
}
@ -152,13 +116,14 @@ Accessing biases:\n\
/// Load an input state file
if (cmd == "load") {
if (argc < 3) {
result = "Missing arguments";
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;
}
}
@ -197,27 +162,28 @@ Accessing biases:\n\
result = cvm::to_str(f);
return COLVARSCRIPT_OK;
} else {
result = "Wrong arguments to command \"frame\"";
result = "Wrong arguments to command \"frame\"\n" + help_string();
return COLVARSCRIPT_ERROR;
}
}
result = "Syntax 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;
}
if (argc < 3) {
result = "Missing parameters";
return COLVARSCRIPT_ERROR;
}
std::string subcmd = argv[2];
if (subcmd == "value") {
@ -261,7 +227,7 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
if (subcmd == "addforce") {
if (argc < 4) {
result = "addforce: missing parameter: force value";
result = "addforce: missing parameter: force value\n" + help_string();
return COLVARSCRIPT_ERROR;
}
std::string f_str = argv[3];
@ -279,12 +245,17 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
result = "Syntax error";
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) {
@ -292,10 +263,6 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
return COLVARSCRIPT_ERROR;
}
if (argc < 3) {
result = "Missing parameters";
return COLVARSCRIPT_ERROR;
}
std::string subcmd = argv[2];
if (subcmd == "energy") {
@ -362,9 +329,55 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
result = "Syntax error";
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}
result = "Syntax 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;
}

4
lib/colvars/colvarscript.h
View File

@ -36,11 +36,15 @@ public:
/// Run script command with given positional arguments
int run(int argc, char const *argv[]);
private:
/// Run subcommands on colvar
int proc_colvar(int argc, char const *argv[]);
/// Run subcommands on bias
int proc_bias(int argc, char const *argv[]);
/// Builds and return a short help
std::string help_string(void);
};