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Update Colvars library to version 2023-05-01

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This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
2023-05-17 13:29:00 -04:00
parent 166301180b
commit 377c652a83
53 changed files with 2575 additions and 2273 deletions
Download Patch File Download Diff File Expand all files Collapse all files

95
lib/colvars/colvarscript_commands.h
View File

@ -134,11 +134,19 @@ CVSCRIPT(cv_config,
char const *conf_str =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
std::string const conf(conf_str);
if (cvm::main()->read_config_string(conf) == COLVARS_OK) {
return COLVARS_OK;
script->proxy()->add_config("config", conf);
if (script->proxy()->engine_ready()) {
// Engine allows immediate initialization
if ((script->proxy()->parse_module_config() |
script->proxy()->setup()) == COLVARS_OK) {
return COLVARS_OK;
} else {
script->add_error_msg("Error parsing configuration string");
return COLVARSCRIPT_ERROR;
}
}
script->add_error_msg("Error parsing configuration string");
return COLVARSCRIPT_ERROR;
// Engine not ready, config will be read during proxy->setup()
return COLVARS_OK;
)
CVSCRIPT(cv_configfile,
@ -146,13 +154,20 @@ CVSCRIPT(cv_configfile,
1, 1,
"conf_file : string - Path to configuration file",
char const *conf_file_name =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
if (script->module()->read_config_file(conf_file_name) == COLVARS_OK) {
return COLVARS_OK;
} else {
script->add_error_msg("Error parsing configuration file");
return COLVARSCRIPT_ERROR;
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
script->proxy()->add_config("configfile", std::string(conf_file_name));
if (script->proxy()->engine_ready()) {
// Engine allows immediate initialization
if ((script->proxy()->parse_module_config() |
script->proxy()->setup()) == COLVARS_OK) {
return COLVARS_OK;
} else {
script->add_error_msg("Error parsing configuration file");
return COLVARSCRIPT_ERROR;
}
}
// Engine not ready, config will be read during proxy->setup()
return COLVARS_OK;
)
CVSCRIPT(cv_delete,
@ -309,6 +324,51 @@ CVSCRIPT(cv_getenergy,
return COLVARS_OK;
)
CVSCRIPT(cv_getnumactiveatomgroups,
"Get the number of atom groups that currently have positive ref counts\n"
"count : integer - Total number of atom groups",
0, 0,
"",
script->set_result_int(static_cast<int>(script->proxy()->get_num_active_atom_groups()));
return COLVARS_OK;
)
CVSCRIPT(cv_getnumactiveatoms,
"Get the number of atoms that currently have positive ref counts\n"
"count : integer - Total number of atoms",
0, 0,
"",
script->set_result_int(static_cast<int>(script->proxy()->get_num_active_atoms()));
return COLVARS_OK;
)
CVSCRIPT(cv_getnumatoms,
"Get the number of requested atoms, including those not in use now\n"
"count : integer - Total number of atoms",
0, 0,
"",
script->set_result_int(static_cast<int>(script->proxy()->get_atom_ids()->size()));
return COLVARS_OK;
)
CVSCRIPT(cv_getstepabsolute,
"Get the current step number of the simulation (including restarts)\n"
"step : int - Absolute step number",
0, 0,
"",
script->set_result_int(cvm::step_absolute());
return COLVARS_OK;
)
CVSCRIPT(cv_getsteprelative,
"Get the current step number from the start of this job\n"
"step : int - Relative step number",
0, 0,
"",
script->set_result_int(cvm::step_relative());
return COLVARS_OK;
)
CVSCRIPT(cv_help,
"Get the help string of the Colvars scripting interface\n"
"help : string - Help string",
@ -481,6 +541,7 @@ CVSCRIPT(cv_reset,
"Delete all internal configuration",
0, 0,
"",
cvm::log("Resetting the Collective Variables module.");
return script->module()->reset();
)
@ -516,6 +577,20 @@ CVSCRIPT(cv_savetostring,
return script->module()->write_restart_string(script->modify_str_result());
)
CVSCRIPT(cv_targettemperature,
"Get/set target temperature, overriding what the MD engine provides\n"
"T : float - Current target temperature in K",
0, 1,
"T : float - New target temperature in K",
char const *Targ =
script->obj_to_str(script->get_module_cmd_arg(0, objc, objv));
if (Targ == NULL) {
return script->set_result_real(script->proxy()->target_temperature());
} else {
return script->proxy()->set_target_temperature(strtod(Targ, NULL));
}
)
CVSCRIPT(cv_units,
"Get or set the current Colvars unit system\n"
"units : string - The current unit system",