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Update Colvars to version 2020-02-27

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This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
This commit is contained in:
Giacomo Fiorin
2020-02-27 19:44:33 -05:00
parent 6e7e365981
commit 7be004512f
24 changed files with 508 additions and 365 deletions
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103
lib/colvars/colvarmodule.cpp
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@ -1284,7 +1284,7 @@ std::istream & colvarmodule::read_restart(std::istream &is)
{
// read global restart information
std::string restart_conf;
if (is >> colvarparse::read_block("configuration", restart_conf)) {
if (is >> colvarparse::read_block("configuration", &restart_conf)) {
parse->get_keyval(restart_conf, "step",
it_restart, static_cast<step_number>(0),
@ -1329,30 +1329,84 @@ std::istream & colvarmodule::read_restart(std::istream &is)
parse->clear_keyword_registry();
}
// colvars restart
cvm::increase_depth();
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
if ( !((*cvi)->read_restart(is)) ) {
cvm::error("Error: in reading restart configuration for collective variable \""+
(*cvi)->name+"\".\n",
INPUT_ERROR);
print_total_forces_errning(warn_total_forces);
read_objects_state(is);
return is;
}
std::istream & colvarmodule::read_objects_state(std::istream &is)
{
size_t pos = 0;
std::string word;
while (is.good()) {
pos = is.tellg();
word.clear();
is >> word;
if (word.size()) {
is.seekg(pos, std::ios::beg);
if (word == "colvar") {
cvm::increase_depth();
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
if ( !((*cvi)->read_state(is)) ) {
// Here an error signals that the variable is a match, but the
// state is corrupt; otherwise, the variable rewinds is silently
cvm::error("Error: in reading restart configuration for "
"collective variable \""+(*cvi)->name+"\".\n",
INPUT_ERROR);
}
if (static_cast<size_t>(is.tellg()) > pos) break; // found it
}
cvm::decrease_depth();
} else {
cvm::increase_depth();
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
if (((*bi)->state_keyword != word) && (*bi)->bias_type != word) {
// Skip biases with different type; state_keyword is used to
// support different versions of the state file format
continue;
}
if (!((*bi)->read_state(is))) {
// Same as above, an error means a match but the state is incorrect
cvm::error("Error: in reading restart configuration for bias \""+
(*bi)->name+"\".\n",
INPUT_ERROR);
}
if (static_cast<size_t>(is.tellg()) > pos) break; // found it
}
cvm::decrease_depth();
}
}
if (static_cast<size_t>(is.tellg()) == pos) {
// This block has not been read by any object: discard it and move on
// to the next one
is >> colvarparse::read_block(word, NULL);
}
if (!is) break;
}
// biases restart
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
if (!((*bi)->read_state(is))) {
cvm::error("Error: in reading restart configuration for bias \""+
(*bi)->name+"\".\n",
INPUT_ERROR);
}
}
cvm::decrease_depth();
return is;
}
int colvarmodule::print_total_forces_errning(bool warn_total_forces)
{
if (warn_total_forces) {
cvm::log(cvm::line_marker);
cvm::log("WARNING: The definition of system forces has changed. Please see:\n");
@ -1367,10 +1421,11 @@ to:\n\
and load it to continue this simulation.\n");
output_prefix() = output_prefix()+".tmp";
write_restart_file(output_prefix()+".colvars.state");
cvm::error("Exiting with error until issue is addressed.\n", INPUT_ERROR);
return cvm::error("Exiting with error until issue is addressed.\n",
INPUT_ERROR);
}
return is;
return COLVARS_OK;
}
@ -1499,7 +1554,7 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
(*cvi)->write_restart(os);
(*cvi)->write_state(os);
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();