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Small fixes to Colvars library

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Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
This commit is contained in:
Giacomo Fiorin
2018-05-02 14:57:41 -04:00
parent d5ec76290b
commit 0c005f5cb0
21 changed files with 605 additions and 452 deletions
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157
lib/colvars/colvarmodule.cpp
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@ -30,10 +30,10 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
depth_s = 0;
cv_traj_os = NULL;
// pointer to the proxy object
if (proxy == NULL) {
proxy = proxy_in;
parse = new colvarparse();
proxy = proxy_in; // Pointer to the proxy object
parse = new colvarparse(); // Parsing object for global options
version_int = proxy->get_version_from_string(COLVARS_VERSION);
} else {
// TODO relax this error to handle multiple molecules in VMD
// once the module is not static anymore
@ -58,22 +58,24 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
// "it_restart" will be set by the input state file, if any;
// "it" should be updated by the proxy
colvarmodule::it = colvarmodule::it_restart = 0;
colvarmodule::it_restart_from_state_file = true;
colvarmodule::use_scripted_forces = false;
use_scripted_forces = false;
scripting_after_biases = false;
colvarmodule::b_analysis = false;
b_analysis = false;
colvarmodule::debug_gradients_step_size = 1.0e-07;
colvarmodule::rotation::monitor_crossings = false;
colvarmodule::rotation::crossing_threshold = 1.0e-02;
colvarmodule::cv_traj_freq = 100;
colvarmodule::restart_out_freq = proxy->restart_frequency();
cv_traj_freq = 100;
restart_out_freq = proxy->restart_frequency();
// by default overwrite the existing trajectory file
colvarmodule::cv_traj_append = false;
cv_traj_append = false;
cv_traj_write_labels = true;
}
@ -189,26 +191,27 @@ int colvarmodule::parse_config(std::string &conf)
{
extra_conf.clear();
// parse global options
// Parse global options
if (catch_input_errors(parse_global_params(conf))) {
return get_error();
}
// parse the options for collective variables
// Parse the options for collective variables
if (catch_input_errors(parse_colvars(conf))) {
return get_error();
}
// parse the options for biases
// Parse the options for biases
if (catch_input_errors(parse_biases(conf))) {
return get_error();
}
// done parsing known keywords, check that all keywords found were valid ones
// Done parsing known keywords, check that all keywords found were valid ones
if (catch_input_errors(parse->check_keywords(conf, "colvarmodule"))) {
return get_error();
}
// Parse auto-generated configuration (e.g. for back-compatibility)
if (extra_conf.size()) {
catch_input_errors(parse_global_params(extra_conf));
catch_input_errors(parse_colvars(extra_conf));
@ -222,13 +225,11 @@ int colvarmodule::parse_config(std::string &conf)
cvm::log("Collective variables module (re)initialized.\n");
cvm::log(cvm::line_marker);
// update any necessary proxy data
// Update any necessary proxy data
proxy->setup();
if (cv_traj_os != NULL) {
// configuration might have changed, better redo the labels
write_traj_label(*cv_traj_os);
}
// configuration might have changed, better redo the labels
cv_traj_write_labels = true;
return get_error();
}
@ -279,15 +280,18 @@ int colvarmodule::parse_global_params(std::string const &conf)
parse->get_keyval(conf, "colvarsTrajAppend",
cv_traj_append, cv_traj_append, colvarparse::parse_silent);
parse->get_keyval(conf, "scriptedColvarForces", use_scripted_forces, false);
parse->get_keyval(conf, "scriptedColvarForces",
use_scripted_forces, use_scripted_forces);
parse->get_keyval(conf, "scriptingAfterBiases", scripting_after_biases, true);
parse->get_keyval(conf, "scriptingAfterBiases",
scripting_after_biases, scripting_after_biases);
if (use_scripted_forces && !proxy->force_script_defined) {
cvm::error("User script for scripted colvar forces not found.", INPUT_ERROR);
return cvm::error("User script for scripted colvar forces not found.",
INPUT_ERROR);
}
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
return cvm::get_error();
}
@ -432,13 +436,13 @@ int colvarmodule::parse_biases(std::string const &conf)
}
int colvarmodule::num_variables() const
size_t colvarmodule::num_variables() const
{
return colvars.size();
}
int colvarmodule::num_variables_feature(int feature_id) const
size_t colvarmodule::num_variables_feature(int feature_id) const
{
size_t n = 0;
for (std::vector<colvar *>::const_iterator cvi = colvars.begin();
@ -452,13 +456,13 @@ int colvarmodule::num_variables_feature(int feature_id) const
}
int colvarmodule::num_biases() const
size_t colvarmodule::num_biases() const
{
return biases.size();
}
int colvarmodule::num_biases_feature(int feature_id) const
size_t colvarmodule::num_biases_feature(int feature_id) const
{
size_t n = 0;
for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
@ -472,7 +476,7 @@ int colvarmodule::num_biases_feature(int feature_id) const
}
int colvarmodule::num_biases_type(std::string const &type) const
size_t colvarmodule::num_biases_type(std::string const &type) const
{
size_t n = 0;
for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
@ -971,13 +975,20 @@ int colvarmodule::write_restart_file(std::string const &out_name)
int colvarmodule::write_traj_files()
{
if (cv_traj_os == NULL) {
open_traj_file(cv_traj_name);
if (open_traj_file(cv_traj_name) != COLVARS_OK) {
return cvm::get_error();
} else {
cv_traj_write_labels = true;
}
}
// write labels in the traj file every 1000 lines and at first timestep
if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) {
if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 ||
cvm::step_relative() == 0 ||
cv_traj_write_labels) {
write_traj_label(*cv_traj_os);
}
cv_traj_write_labels = false;
if ((cvm::step_absolute() % cv_traj_freq) == 0) {
write_traj(*cv_traj_os);
@ -1064,7 +1075,7 @@ int colvarmodule::reset()
{
parse->init();
cvm::log("Resetting the Collective Variables Module.\n");
cvm::log("Resetting the Collective Variables module.\n");
// Iterate backwards because we are deleting the elements as we go
for (std::vector<colvarbias *>::reverse_iterator bi = biases.rbegin();
@ -1073,6 +1084,7 @@ int colvarmodule::reset()
delete *bi; // the bias destructor updates the biases array
}
biases.clear();
biases_active_.clear();
// Iterate backwards because we are deleting the elements as we go
for (std::vector<colvar *>::reverse_iterator cvi = colvars.rbegin();
@ -1088,7 +1100,7 @@ int colvarmodule::reset()
proxy->reset();
if (cv_traj_os != NULL) {
// Do not close file here, as we might not be done with it yet.
// Do not close traj file here, as we might not be done with it yet.
proxy->flush_output_stream(cv_traj_os);
}
@ -1188,12 +1200,10 @@ 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 (it_restart_from_state_file) {
parse->get_keyval(restart_conf, "step",
it_restart, (size_t) 0,
colvarparse::parse_silent);
parse->get_keyval(restart_conf, "step",
it_restart, (size_t) 0,
colvarparse::parse_silent);
it = it_restart;
}
std::string restart_version;
parse->get_keyval(restart_conf, "version",
restart_version, std::string(""),
@ -1688,40 +1698,59 @@ int cvm::read_index_file(char const *filename)
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
}
int cvm::load_atoms(char const *file_name,
cvm::atom_group &atoms,
std::string const &pdb_field,
double const pdb_field_value)
double pdb_field_value)
{
return proxy->load_atoms(file_name, atoms, pdb_field, pdb_field_value);
}
int cvm::load_coords(char const *file_name,
std::vector<cvm::atom_pos> &pos,
const std::vector<int> &indices,
std::string const &pdb_field,
double const pdb_field_value)
{
// Differentiate between PDB and XYZ files
// for XYZ files, use CVM internal parser
// otherwise call proxy function for PDB
std::string const ext(strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name);
int cvm::load_coords(char const *file_name,
std::vector<cvm::rvector> *pos,
cvm::atom_group *atoms,
std::string const &pdb_field,
double pdb_field_value)
{
int error_code = COLVARS_OK;
std::string const ext(strlen(file_name) > 4 ?
(file_name + (strlen(file_name) - 4)) :
file_name);
atoms->create_sorted_ids();
std::vector<cvm::rvector> sorted_pos(atoms->size(), cvm::rvector(0.0));
// Differentiate between PDB and XYZ files
if (colvarparse::to_lower_cppstr(ext) == std::string(".xyz")) {
if ( pdb_field.size() > 0 ) {
cvm::error("Error: PDB column may not be specified for XYZ coordinate file.\n", INPUT_ERROR);
return COLVARS_ERROR;
if (pdb_field.size() > 0) {
return cvm::error("Error: PDB column may not be specified "
"for XYZ coordinate files.\n", INPUT_ERROR);
}
return cvm::load_coords_xyz(file_name, pos, indices);
// For XYZ files, use internal parser
error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms);
} else {
return proxy->load_coords(file_name, pos, indices, pdb_field, pdb_field_value);
// Otherwise, call proxy function for PDB
error_code |= proxy->load_coords(file_name,
sorted_pos, atoms->sorted_ids(),
pdb_field, pdb_field_value);
}
std::vector<int> const &map = atoms->sorted_ids_map();
for (size_t i = 0; i < atoms->size(); i++) {
(*pos)[map[i]] = sorted_pos[i];
}
return error_code;
}
int cvm::load_coords_xyz(char const *filename,
std::vector<atom_pos> &pos,
const std::vector<int> &indices)
std::vector<rvector> *pos,
cvm::atom_group *atoms)
{
std::ifstream xyz_is(filename);
unsigned int natoms;
@ -1736,12 +1765,12 @@ int cvm::load_coords_xyz(char const *filename,
cvm::getline(xyz_is, line);
cvm::getline(xyz_is, line);
xyz_is.width(255);
std::vector<atom_pos>::iterator pos_i = pos.begin();
std::vector<atom_pos>::iterator pos_i = pos->begin();
if (pos.size() != natoms) { // Use specified indices
if (pos->size() != natoms) { // Use specified indices
int next = 0; // indices are zero-based
std::vector<int>::const_iterator index = indices.begin();
for ( ; pos_i != pos.end() ; pos_i++, index++) {
std::vector<int>::const_iterator index = atoms->sorted_ids().begin();
for ( ; pos_i != pos->end() ; pos_i++, index++) {
while ( next < *index ) {
cvm::getline(xyz_is, line);
@ -1751,7 +1780,7 @@ int cvm::load_coords_xyz(char const *filename,
xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
}
} else { // Use all positions
for ( ; pos_i != pos.end() ; pos_i++) {
for ( ; pos_i != pos->end() ; pos_i++) {
xyz_is >> symbol;
xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
}
@ -1792,17 +1821,13 @@ void cvm::request_total_force()
proxy->request_total_force(true);
}
cvm::rvector cvm::position_distance(atom_pos const &pos1,
atom_pos const &pos2)
cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
return proxy->position_distance(pos1, pos2);
}
cvm::real cvm::position_dist2(cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
return proxy->position_dist2(pos1, pos2);
}
cvm::real cvm::rand_gaussian(void)
{