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Update Colvars library to version 2024-06-04

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This commit is contained in:
Giacomo Fiorin
2024-08-06 01:07:43 +02:00
parent 278accd9ea
commit 133dee9ac1
74 changed files with 7343 additions and 4676 deletions
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62
lib/colvars/colvarscript_commands.h
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@ -47,14 +47,10 @@
// If CVSCRIPT is not defined, this file yields the function prototypes
#ifndef CVSCRIPT
#ifdef __cplusplus
#define CVSCRIPT_COMM_PROTO(COMM) \
extern "C" int CVSCRIPT_COMM_FNAME(COMM)(void *, \
int, unsigned char *const *);
#else
#define CVSCRIPT_COMM_PROTO(COMM) \
int CVSCRIPT_COMM_FNAME(COMM)(void *, int, unsigned char *const *);
#endif
int, \
unsigned char *const *);
#define CVSCRIPT(COMM,HELP,N_ARGS_MIN,N_ARGS_MAX,ARGS,FN_BODY) \
CVSCRIPT_COMM_PROTO(COMM)
@ -454,7 +450,8 @@ CVSCRIPT(cv_listcommands,
)
CVSCRIPT(cv_listindexfiles,
"Get a list of the index files loaded in this session",
"Get a list of the index files loaded in this session\n"
"list : sequence of strings - List of index file names",
0, 0,
"",
int const n_files = script->module()->index_file_names.size();
@ -467,19 +464,36 @@ CVSCRIPT(cv_listindexfiles,
return COLVARS_OK;
)
CVSCRIPT(cv_listinputfiles,
"Get a list of all input/configuration files loaded in this session\n"
"list : sequence of strings - List of file names",
0, 0,
"",
std::list<std::string> const l =
script->proxy()->list_input_stream_names();
std::string result;
for (std::list<std::string>::const_iterator li = l.begin();
li != l.end(); li++) {
if (li != l.begin()) result.append(1, ' ');
result.append(*li);
}
script->set_result_str(result);
return COLVARS_OK;
)
CVSCRIPT(cv_load,
"Load data from a state file into all matching colvars and biases",
1, 1,
"prefix : string - Path to existing state file or input prefix",
char const *arg =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
script->proxy()->input_prefix() = cvm::state_file_prefix(arg);
if (script->module()->setup_input() == COLVARS_OK) {
return COLVARS_OK;
} else {
int error_code =
script->proxy()->set_input_prefix(cvm::state_file_prefix(arg));
error_code |= script->module()->setup_input();
if (error_code != COLVARS_OK) {
script->add_error_msg("Error loading state file");
return COLVARSCRIPT_ERROR;
}
return error_code;
)
CVSCRIPT(cv_loadfromstring,
@ -488,7 +502,8 @@ CVSCRIPT(cv_loadfromstring,
"buffer : string - String buffer containing the state information",
char const *arg =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
script->proxy()->input_buffer() = arg;
script->proxy()->input_stream_from_string("input state string",
std::string(arg));
if (script->module()->setup_input() == COLVARS_OK) {
return COLVARS_OK;
} else {
@ -560,8 +575,7 @@ CVSCRIPT(cv_save,
"prefix : string - Output prefix with trailing \".colvars.state\" gets removed)",
std::string const prefix =
cvm::state_file_prefix(script->obj_to_str(script->get_module_cmd_arg(0, objc, objv)));
script->proxy()->output_prefix() = prefix;
int error_code = COLVARS_OK;
int error_code = script->proxy()->set_output_prefix(prefix);
error_code |= script->module()->setup_output();
error_code |= script->module()->write_restart_file(prefix+
".colvars.state");
@ -578,10 +592,10 @@ CVSCRIPT(cv_savetostring,
)
CVSCRIPT(cv_targettemperature,
"Get/set target temperature, overriding what the MD engine provides\n"
"Get/set target temperature, overriding internally what the MD engine reports\n"
"T : float - Current target temperature in K",
0, 1,
"T : float - New target temperature in K",
"T : float - New target temperature in K (internal use)",
char const *Targ =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
if (Targ == NULL) {
@ -591,6 +605,20 @@ CVSCRIPT(cv_targettemperature,
}
)
CVSCRIPT(cv_timestep,
"Get/set integration timestep, overriding internally what the MD engine reports\n"
"dt : float - Current integration timestep in MD engine units",
0, 1,
"dt : float - New integration timestep in MD engine units",
char const *arg =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
if (arg == NULL) {
return script->set_result_real(script->proxy()->dt());
} else {
return script->proxy()->set_integration_timestep(strtod(arg, NULL));
}
)
CVSCRIPT(cv_units,
"Get or set the current Colvars unit system\n"
"units : string - The current unit system",