1220bea011
This update includes one new feature (neural-network based collective variables), several small enhancements (including an automatic definition of grid boundaries for angle-based CVs, and a normalization option for eigenvector-based CVs), bugfixes and documentation improvements. Usage information for specific features included in the Colvars library (i.e. not just the library as a whole) is now also reported to the screen or LAMMPS logfile (as is done already in other LAMMPS classes). Notable to LAMMPS code development are the removals of duplicated code and of ambiguously-named preprocessor defines in the Colvars headers. Since the last PR, the existing regression tests have also been running automatically via GitHub Actions. The following pull requests in the Colvars repository are relevant to LAMMPS: - 475 Remove fatal error condition https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin) - 474 Allow normalizing eigenvector vector components to deal with unit change https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin) - 470 Better error handling in the initialization of NeuralNetwork CV https://github.com/Colvars/colvars/pull/470 (@HanatoK) - 468 Add examples of histogram configuration, with and without explicit grid parameters https://github.com/Colvars/colvars/pull/468 (@giacomofiorin) - 464 Fix #463 using more fine-grained features https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin) - 447 [RFC] New option "scaledBiasingForce" for colvarbias https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin) - 444 [RFC] Implementation of dense neural network as CV https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin) - 443 Fix explicit gradient dependency of sub-CVs https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin) - 442 Persistent bias count https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin) - 437 Return type of bias from scripting interface https://github.com/Colvars/colvars/pull/437 (@giacomofiorin) - 434 More flexible use of boundaries from colvars by grids https://github.com/Colvars/colvars/pull/434 (@jhenin) - 433 Prevent double-free in linearCombination https://github.com/Colvars/colvars/pull/433 (@HanatoK) - 428 More complete documentation for index file format (NDX) https://github.com/Colvars/colvars/pull/428 (@giacomofiorin) - 426 Integrate functional version of backup_file() into base proxy class https://github.com/Colvars/colvars/pull/426 (@giacomofiorin) - 424 Track CVC inheritance when documenting feature usage https://github.com/Colvars/colvars/pull/424 (@giacomofiorin) - 419 Generate citation report while running computations https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin) - 415 Rebin metadynamics bias from explicit hills when available https://github.com/Colvars/colvars/pull/415 (@giacomofiorin) - 312 Ignore a keyword if it has content to the left of it (regardless of braces) https://github.com/Colvars/colvars/pull/312 (@giacomofiorin) Authors: @giacomofiorin, @HanatoK, @jhenin
2420 lines
65 KiB
C++
2420 lines
65 KiB
C++
// -*- c++ -*-
|
|
|
|
// This file is part of the Collective Variables module (Colvars).
|
|
// The original version of Colvars and its updates are located at:
|
|
// https://github.com/Colvars/colvars
|
|
// Please update all Colvars source files before making any changes.
|
|
// If you wish to distribute your changes, please submit them to the
|
|
// Colvars repository at GitHub.
|
|
|
|
#include <sstream>
|
|
#include <cstring>
|
|
#include <vector>
|
|
#include <map>
|
|
|
|
#include "colvarmodule.h"
|
|
#include "colvarparse.h"
|
|
#include "colvarproxy.h"
|
|
#include "colvar.h"
|
|
#include "colvarbias.h"
|
|
#include "colvarbias_abf.h"
|
|
#include "colvarbias_alb.h"
|
|
#include "colvarbias_histogram.h"
|
|
#include "colvarbias_histogram_reweight_amd.h"
|
|
#include "colvarbias_meta.h"
|
|
#include "colvarbias_restraint.h"
|
|
#include "colvarscript.h"
|
|
#include "colvaratoms.h"
|
|
#include "colvarcomp.h"
|
|
|
|
|
|
|
|
/// Track usage of Colvars features
|
|
class colvarmodule::usage {
|
|
|
|
public:
|
|
|
|
/// Constructor
|
|
usage();
|
|
|
|
/// Increment usage count for the given feature; return error if not found
|
|
int cite_feature(std::string const &feature);
|
|
|
|
/// Increment usage count for the given paper; return error if not found
|
|
int cite_paper(std::string const &paper);
|
|
|
|
/// Generate a report for used features (0 = URL, 1 = BibTeX)
|
|
std::string report(int flag);
|
|
|
|
protected:
|
|
|
|
/// Usage count for each feature
|
|
std::map<std::string, int> feature_count_;
|
|
|
|
/// Usage count for each cited paper
|
|
std::map<std::string, int> paper_count_;
|
|
|
|
/// URL for each paper
|
|
std::map<std::string, std::string> paper_url_;
|
|
|
|
/// BibTeX entry for each paper
|
|
std::map<std::string, std::string> paper_bibtex_;
|
|
|
|
/// Map code features to the relevant papers
|
|
std::map<std::string, std::string> feature_paper_map_;
|
|
|
|
};
|
|
|
|
|
|
colvarmodule::colvarmodule(colvarproxy *proxy_in)
|
|
{
|
|
depth_s = 0;
|
|
log_level_ = 10;
|
|
|
|
cv_traj_os = NULL;
|
|
|
|
xyz_reader_use_count = 0;
|
|
|
|
num_biases_types_used_ =
|
|
reinterpret_cast<void *>(new std::map<std::string, int>());
|
|
|
|
restart_version_str.clear();
|
|
restart_version_int = 0;
|
|
|
|
usage_ = new usage();
|
|
usage_->cite_feature("Colvars module");
|
|
|
|
if (proxy != NULL) {
|
|
// TODO relax this error to handle multiple molecules in VMD
|
|
// once the module is not static anymore
|
|
cvm::error("Error: trying to allocate the collective "
|
|
"variable module twice.\n", COLVARS_BUG_ERROR);
|
|
return;
|
|
}
|
|
|
|
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);
|
|
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Initializing the collective variables module, version "+
|
|
version()+".\n");
|
|
cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n"
|
|
" https://doi.org/10.1080/00268976.2013.813594\n"
|
|
"as well as all other papers listed below for individual features used.\n");
|
|
|
|
if (proxy->smp_enabled() == COLVARS_OK) {
|
|
cvm::log("SMP parallelism is enabled; if needed, use \"smp off\" to override this.\n");
|
|
}
|
|
|
|
#if (__cplusplus >= 201103L)
|
|
cvm::log("This version was built with the C++11 standard or higher.\n");
|
|
#else
|
|
cvm::log("This version was built without the C++11 standard: some features are disabled.\n"
|
|
"Please see the following link for details:\n"
|
|
" https://colvars.github.io/README-c++11.html\n");
|
|
#endif
|
|
|
|
// set initial default values
|
|
|
|
// "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;
|
|
|
|
use_scripted_forces = false;
|
|
scripting_after_biases = false;
|
|
|
|
colvarmodule::debug_gradients_step_size = 1.0e-07;
|
|
|
|
colvarmodule::rotation::monitor_crossings = false;
|
|
colvarmodule::rotation::crossing_threshold = 1.0e-02;
|
|
|
|
cv_traj_freq = 100;
|
|
restart_out_freq = proxy->default_restart_frequency();
|
|
|
|
// by default overwrite the existing trajectory file
|
|
cv_traj_append = false;
|
|
cv_traj_write_labels = true;
|
|
|
|
// Removes the need for proxy specializations to create this
|
|
proxy->script = new colvarscript(proxy, this);
|
|
}
|
|
|
|
|
|
colvarmodule * colvarmodule::main()
|
|
{
|
|
return proxy ? proxy->colvars : NULL;
|
|
}
|
|
|
|
|
|
std::vector<colvar *> *colvarmodule::variables()
|
|
{
|
|
return &colvars;
|
|
}
|
|
|
|
|
|
std::vector<colvar *> *colvarmodule::variables_active()
|
|
{
|
|
return &colvars_active;
|
|
}
|
|
|
|
|
|
std::vector<colvar *> *colvarmodule::variables_active_smp()
|
|
{
|
|
return &colvars_smp;
|
|
}
|
|
|
|
|
|
std::vector<int> *colvarmodule::variables_active_smp_items()
|
|
{
|
|
return &colvars_smp_items;
|
|
}
|
|
|
|
|
|
std::vector<colvarbias *> *colvarmodule::biases_active()
|
|
{
|
|
return &(biases_active_);
|
|
}
|
|
|
|
|
|
size_t colvarmodule::size() const
|
|
{
|
|
return colvars.size() + biases.size();
|
|
}
|
|
|
|
|
|
int colvarmodule::read_config_file(char const *config_filename)
|
|
{
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Reading new configuration from file \""+
|
|
std::string(config_filename)+"\":\n");
|
|
|
|
// open the configfile
|
|
config_s.open(config_filename);
|
|
if (!config_s.is_open()) {
|
|
cvm::error("Error: in opening configuration file \""+
|
|
std::string(config_filename)+"\".\n",
|
|
COLVARS_FILE_ERROR);
|
|
return COLVARS_ERROR;
|
|
}
|
|
|
|
// read the config file into a string
|
|
std::string conf = "";
|
|
std::string line;
|
|
while (parse->read_config_line(config_s, line)) {
|
|
// Delete lines that contain only white space after removing comments
|
|
if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
|
|
conf.append(line+"\n");
|
|
}
|
|
config_s.close();
|
|
|
|
return parse_config(conf);
|
|
}
|
|
|
|
|
|
int colvarmodule::read_config_string(std::string const &config_str)
|
|
{
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Reading new configuration:\n");
|
|
std::istringstream new_config_s(config_str);
|
|
|
|
// strip the comments away
|
|
std::string conf = "";
|
|
std::string line;
|
|
while (parse->read_config_line(new_config_s, line)) {
|
|
// Delete lines that contain only white space after removing comments
|
|
if (line.find_first_not_of(colvarparse::white_space) != std::string::npos)
|
|
conf.append(line+"\n");
|
|
}
|
|
|
|
return parse_config(conf);
|
|
}
|
|
|
|
|
|
std::istream & colvarmodule::getline(std::istream &is, std::string &line)
|
|
{
|
|
std::string l;
|
|
if (std::getline(is, l)) {
|
|
size_t const sz = l.size();
|
|
if (sz > 0) {
|
|
if (l[sz-1] == '\r' ) {
|
|
// Replace Windows newlines with Unix newlines
|
|
line = l.substr(0, sz-1);
|
|
} else {
|
|
line = l;
|
|
}
|
|
} else {
|
|
line.clear();
|
|
}
|
|
}
|
|
return is;
|
|
}
|
|
|
|
|
|
int colvarmodule::parse_config(std::string &conf)
|
|
{
|
|
// Auto-generated additional configuration
|
|
extra_conf.clear();
|
|
|
|
// Check that the input has matching braces
|
|
if (colvarparse::check_braces(conf, 0) != COLVARS_OK) {
|
|
return cvm::error("Error: unmatched curly braces in configuration.\n",
|
|
COLVARS_INPUT_ERROR);
|
|
}
|
|
|
|
// Check that the input has only ASCII characters, and warn otherwise
|
|
colvarparse::check_ascii(conf);
|
|
|
|
// Parse global options
|
|
if (catch_input_errors(parse_global_params(conf))) {
|
|
return get_error();
|
|
}
|
|
|
|
// Parse the options for collective variables
|
|
if (catch_input_errors(parse_colvars(conf))) {
|
|
return get_error();
|
|
}
|
|
|
|
// 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
|
|
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));
|
|
catch_input_errors(parse_biases(extra_conf));
|
|
parse->check_keywords(extra_conf, "colvarmodule");
|
|
extra_conf.clear();
|
|
if (get_error() != COLVARS_OK) return get_error();
|
|
}
|
|
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Collective variables module (re)initialized.\n");
|
|
cvm::log(cvm::line_marker);
|
|
|
|
// Update any necessary proxy data
|
|
proxy->setup();
|
|
|
|
if (source_Tcl_script.size() > 0) {
|
|
run_tcl_script(source_Tcl_script);
|
|
}
|
|
|
|
return get_error();
|
|
}
|
|
|
|
|
|
std::string const & colvarmodule::get_config() const
|
|
{
|
|
return parse->get_config();
|
|
}
|
|
|
|
|
|
int colvarmodule::append_new_config(std::string const &new_conf)
|
|
{
|
|
extra_conf += new_conf;
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
void colvarmodule::config_changed()
|
|
{
|
|
cv_traj_write_labels = true;
|
|
}
|
|
|
|
|
|
int colvarmodule::parse_global_params(std::string const &conf)
|
|
{
|
|
// TODO document and then echo this keyword
|
|
parse->get_keyval(conf, "logLevel", log_level_, log_level_,
|
|
colvarparse::parse_silent);
|
|
{
|
|
std::string units;
|
|
if (parse->get_keyval(conf, "units", units)) {
|
|
units = colvarparse::to_lower_cppstr(units);
|
|
int error_code = proxy->set_unit_system(units, (colvars.size() != 0));
|
|
if (error_code != COLVARS_OK) {
|
|
return error_code;
|
|
}
|
|
}
|
|
}
|
|
|
|
{
|
|
std::string index_file_name;
|
|
size_t pos = 0;
|
|
while (parse->key_lookup(conf, "indexFile", &index_file_name, &pos)) {
|
|
cvm::log("# indexFile = \""+index_file_name+"\"\n");
|
|
read_index_file(index_file_name.c_str());
|
|
index_file_name.clear();
|
|
}
|
|
}
|
|
|
|
if (parse->get_keyval(conf, "smp", proxy->b_smp_active, proxy->b_smp_active)) {
|
|
if (proxy->b_smp_active == false) {
|
|
cvm::log("SMP parallelism has been disabled.\n");
|
|
}
|
|
}
|
|
|
|
bool b_analysis = true;
|
|
if (parse->get_keyval(conf, "analysis", b_analysis, true,
|
|
colvarparse::parse_silent)) {
|
|
cvm::log("Warning: keyword \"analysis\" is deprecated: it is now set "
|
|
"to true; individual analyses are performed only if requested.");
|
|
}
|
|
|
|
parse->get_keyval(conf, "debugGradientsStepSize", debug_gradients_step_size,
|
|
debug_gradients_step_size,
|
|
colvarparse::parse_silent);
|
|
|
|
parse->get_keyval(conf, "monitorEigenvalueCrossing",
|
|
colvarmodule::rotation::monitor_crossings,
|
|
colvarmodule::rotation::monitor_crossings,
|
|
colvarparse::parse_silent);
|
|
parse->get_keyval(conf, "eigenvalueCrossingThreshold",
|
|
colvarmodule::rotation::crossing_threshold,
|
|
colvarmodule::rotation::crossing_threshold,
|
|
colvarparse::parse_silent);
|
|
|
|
parse->get_keyval(conf, "colvarsTrajFrequency", cv_traj_freq, cv_traj_freq);
|
|
parse->get_keyval(conf, "colvarsRestartFrequency",
|
|
restart_out_freq, restart_out_freq);
|
|
|
|
// Deprecate append flag
|
|
parse->get_keyval(conf, "colvarsTrajAppend",
|
|
cv_traj_append, cv_traj_append, colvarparse::parse_silent);
|
|
|
|
parse->get_keyval(conf, "scriptedColvarForces",
|
|
use_scripted_forces, use_scripted_forces);
|
|
|
|
parse->get_keyval(conf, "scriptingAfterBiases",
|
|
scripting_after_biases, scripting_after_biases);
|
|
|
|
#if defined(COLVARS_TCL)
|
|
parse->get_keyval(conf, "sourceTclFile", source_Tcl_script);
|
|
#endif
|
|
|
|
return cvm::get_error();
|
|
}
|
|
|
|
|
|
int colvarmodule::run_tcl_script(std::string const &filename) {
|
|
|
|
int result = COLVARS_OK;
|
|
|
|
#if defined(COLVARS_TCL)
|
|
result = proxy->tcl_run_file(filename);
|
|
#endif
|
|
|
|
return result;
|
|
}
|
|
|
|
|
|
int colvarmodule::parse_colvars(std::string const &conf)
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log("Initializing the collective variables.\n");
|
|
|
|
std::string colvar_conf = "";
|
|
size_t pos = 0;
|
|
while (parse->key_lookup(conf, "colvar", &colvar_conf, &pos)) {
|
|
|
|
if (colvar_conf.size()) {
|
|
cvm::log(cvm::line_marker);
|
|
cvm::increase_depth();
|
|
colvars.push_back(new colvar());
|
|
if (((colvars.back())->init(colvar_conf) != COLVARS_OK) ||
|
|
((colvars.back())->check_keywords(colvar_conf, "colvar") != COLVARS_OK)) {
|
|
cvm::log("Error while constructing colvar number " +
|
|
cvm::to_str(colvars.size()) + " : deleting.");
|
|
delete colvars.back(); // the colvar destructor updates the colvars array
|
|
return COLVARS_ERROR;
|
|
}
|
|
cvm::decrease_depth();
|
|
} else {
|
|
cvm::error("Error: \"colvar\" keyword found without any configuration.\n", COLVARS_INPUT_ERROR);
|
|
return COLVARS_ERROR;
|
|
}
|
|
cvm::decrease_depth();
|
|
colvar_conf = "";
|
|
}
|
|
|
|
if (pos > 0) {
|
|
// One or more new variables were added
|
|
config_changed();
|
|
}
|
|
|
|
if (!colvars.size()) {
|
|
cvm::log("Warning: no collective variables defined.\n");
|
|
}
|
|
|
|
if (colvars.size())
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Collective variables initialized, "+
|
|
cvm::to_str(colvars.size())+
|
|
" in total.\n");
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
bool colvarmodule::check_new_bias(std::string &conf, char const *key)
|
|
{
|
|
if (cvm::get_error() ||
|
|
(biases.back()->check_keywords(conf, key) != COLVARS_OK)) {
|
|
cvm::log("Error while constructing bias number " +
|
|
cvm::to_str(biases.size()) + " : deleting.\n");
|
|
delete biases.back(); // the bias destructor updates the biases array
|
|
return true;
|
|
}
|
|
return false;
|
|
}
|
|
|
|
|
|
template <class bias_type>
|
|
int colvarmodule::parse_biases_type(std::string const &conf,
|
|
char const *keyword)
|
|
{
|
|
// Allow camel case when calling, but use only lower case for parsing
|
|
std::string const &type_keyword = colvarparse::to_lower_cppstr(keyword);
|
|
|
|
// Check how many times this bias keyword was used, set default name
|
|
// accordingly
|
|
std::map<std::string, int> *num_biases_types_used =
|
|
reinterpret_cast<std::map<std::string, int> *>(num_biases_types_used_);
|
|
if (num_biases_types_used->count(type_keyword) == 0) {
|
|
(*num_biases_types_used)[type_keyword] = 0;
|
|
}
|
|
|
|
std::string bias_conf = "";
|
|
size_t conf_saved_pos = 0;
|
|
while (parse->key_lookup(conf, keyword, &bias_conf, &conf_saved_pos)) {
|
|
if (bias_conf.size()) {
|
|
cvm::log(cvm::line_marker);
|
|
cvm::increase_depth();
|
|
int &bias_count = (*num_biases_types_used)[type_keyword];
|
|
biases.push_back(new bias_type(type_keyword.c_str()));
|
|
bias_count += 1;
|
|
biases.back()->rank = bias_count;
|
|
biases.back()->init(bias_conf);
|
|
if (cvm::check_new_bias(bias_conf, keyword) != COLVARS_OK) {
|
|
return COLVARS_ERROR;
|
|
}
|
|
cvm::decrease_depth();
|
|
} else {
|
|
cvm::error("Error: keyword \""+std::string(keyword)+"\" found without configuration.\n",
|
|
COLVARS_INPUT_ERROR);
|
|
return COLVARS_ERROR;
|
|
}
|
|
bias_conf = "";
|
|
}
|
|
if (conf_saved_pos > 0) {
|
|
// One or more new biases were added
|
|
config_changed();
|
|
}
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int colvarmodule::parse_biases(std::string const &conf)
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log("Initializing the collective variables biases.\n");
|
|
|
|
/// initialize ABF instances
|
|
parse_biases_type<colvarbias_abf>(conf, "abf");
|
|
|
|
/// initialize adaptive linear biases
|
|
parse_biases_type<colvarbias_alb>(conf, "ALB");
|
|
|
|
/// initialize harmonic restraints
|
|
parse_biases_type<colvarbias_restraint_harmonic>(conf, "harmonic");
|
|
|
|
/// initialize harmonic walls restraints
|
|
parse_biases_type<colvarbias_restraint_harmonic_walls>(conf, "harmonicWalls");
|
|
|
|
/// initialize histograms
|
|
parse_biases_type<colvarbias_histogram>(conf, "histogram");
|
|
|
|
/// initialize histogram restraints
|
|
parse_biases_type<colvarbias_restraint_histogram>(conf, "histogramRestraint");
|
|
|
|
/// initialize linear restraints
|
|
parse_biases_type<colvarbias_restraint_linear>(conf, "linear");
|
|
|
|
/// initialize metadynamics instances
|
|
parse_biases_type<colvarbias_meta>(conf, "metadynamics");
|
|
|
|
/// initialize reweightaMD instances
|
|
parse_biases_type<colvarbias_reweightaMD>(conf, "reweightaMD");
|
|
|
|
if (use_scripted_forces) {
|
|
cvm::log(cvm::line_marker);
|
|
cvm::increase_depth();
|
|
cvm::log("User forces script will be run at each bias update.\n");
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
std::vector<std::string> const time_biases = time_dependent_biases();
|
|
if (time_biases.size() > 1) {
|
|
cvm::log("WARNING: there are "+cvm::to_str(time_biases.size())+
|
|
" time-dependent biases with non-zero force parameters:\n"+
|
|
cvm::to_str(time_biases)+"\n"+
|
|
"Please ensure that their forces do not counteract each other.\n");
|
|
}
|
|
|
|
if (num_biases() || use_scripted_forces) {
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Collective variables biases initialized, "+
|
|
cvm::to_str(num_biases())+" in total.\n");
|
|
} else {
|
|
if (!use_scripted_forces) {
|
|
cvm::log("No collective variables biases were defined.\n");
|
|
}
|
|
}
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
size_t colvarmodule::num_variables() const
|
|
{
|
|
return colvars.size();
|
|
}
|
|
|
|
|
|
size_t colvarmodule::num_variables_feature(int feature_id) const
|
|
{
|
|
size_t n = 0;
|
|
for (std::vector<colvar *>::const_iterator cvi = colvars.begin();
|
|
cvi != colvars.end();
|
|
cvi++) {
|
|
if ((*cvi)->is_enabled(feature_id)) {
|
|
n++;
|
|
}
|
|
}
|
|
return n;
|
|
}
|
|
|
|
|
|
size_t colvarmodule::num_biases() const
|
|
{
|
|
return biases.size();
|
|
}
|
|
|
|
|
|
size_t colvarmodule::num_biases_feature(int feature_id) const
|
|
{
|
|
size_t n = 0;
|
|
for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
if ((*bi)->is_enabled(feature_id)) {
|
|
n++;
|
|
}
|
|
}
|
|
return n;
|
|
}
|
|
|
|
|
|
size_t colvarmodule::num_biases_type(std::string const &type) const
|
|
{
|
|
size_t n = 0;
|
|
for (std::vector<colvarbias *>::const_iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
if ((*bi)->bias_type == type) {
|
|
n++;
|
|
}
|
|
}
|
|
return n;
|
|
}
|
|
|
|
|
|
std::vector<std::string> const colvarmodule::time_dependent_biases() const
|
|
{
|
|
size_t i;
|
|
std::vector<std::string> biases_names;
|
|
for (i = 0; i < num_biases(); i++) {
|
|
if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
|
|
biases[i]->is_enabled(colvardeps::f_cvb_active) &&
|
|
(biases[i]->is_enabled(colvardeps::f_cvb_history_dependent) ||
|
|
biases[i]->is_enabled(colvardeps::f_cvb_time_dependent))) {
|
|
biases_names.push_back(biases[i]->name);
|
|
}
|
|
}
|
|
return biases_names;
|
|
}
|
|
|
|
|
|
int colvarmodule::catch_input_errors(int result)
|
|
{
|
|
if (result != COLVARS_OK || get_error()) {
|
|
set_error_bits(result);
|
|
set_error_bits(COLVARS_INPUT_ERROR);
|
|
parse->clear();
|
|
return get_error();
|
|
}
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
colvarbias * colvarmodule::bias_by_name(std::string const &name)
|
|
{
|
|
colvarmodule *cv = cvm::main();
|
|
for (std::vector<colvarbias *>::iterator bi = cv->biases.begin();
|
|
bi != cv->biases.end();
|
|
bi++) {
|
|
if ((*bi)->name == name) {
|
|
return (*bi);
|
|
}
|
|
}
|
|
return NULL;
|
|
}
|
|
|
|
|
|
colvar *colvarmodule::colvar_by_name(std::string const &name)
|
|
{
|
|
colvarmodule *cv = cvm::main();
|
|
for (std::vector<colvar *>::iterator cvi = cv->colvars.begin();
|
|
cvi != cv->colvars.end();
|
|
cvi++) {
|
|
if ((*cvi)->name == name) {
|
|
return (*cvi);
|
|
}
|
|
}
|
|
return NULL;
|
|
}
|
|
|
|
|
|
cvm::atom_group *colvarmodule::atom_group_by_name(std::string const &name)
|
|
{
|
|
colvarmodule *cv = cvm::main();
|
|
for (std::vector<cvm::atom_group *>::iterator agi = cv->named_atom_groups.begin();
|
|
agi != cv->named_atom_groups.end();
|
|
agi++) {
|
|
if ((*agi)->name == name) {
|
|
return (*agi);
|
|
}
|
|
}
|
|
return NULL;
|
|
}
|
|
|
|
|
|
void colvarmodule::register_named_atom_group(atom_group *ag) {
|
|
named_atom_groups.push_back(ag);
|
|
}
|
|
|
|
|
|
void colvarmodule::unregister_named_atom_group(cvm::atom_group *ag)
|
|
{
|
|
for (std::vector<cvm::atom_group *>::iterator agi = named_atom_groups.begin();
|
|
agi != named_atom_groups.end();
|
|
agi++) {
|
|
if (*agi == ag) {
|
|
named_atom_groups.erase(agi);
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
int colvarmodule::change_configuration(std::string const &bias_name,
|
|
std::string const &conf)
|
|
{
|
|
// This is deprecated; supported strategy is to delete the bias
|
|
// and parse the new config
|
|
cvm::increase_depth();
|
|
colvarbias *b;
|
|
b = bias_by_name(bias_name);
|
|
if (b == NULL) {
|
|
cvm::error("Error: bias not found: " + bias_name);
|
|
return COLVARS_ERROR;
|
|
}
|
|
b->change_configuration(conf);
|
|
cvm::decrease_depth();
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
std::string colvarmodule::read_colvar(std::string const &name)
|
|
{
|
|
cvm::increase_depth();
|
|
colvar *c;
|
|
std::stringstream ss;
|
|
c = colvar_by_name(name);
|
|
if (c == NULL) {
|
|
cvm::error("Error: colvar not found: " + name);
|
|
return std::string();
|
|
}
|
|
ss << c->value();
|
|
cvm::decrease_depth();
|
|
return ss.str();
|
|
}
|
|
|
|
|
|
cvm::real colvarmodule::energy_difference(std::string const &bias_name,
|
|
std::string const &conf)
|
|
{
|
|
cvm::increase_depth();
|
|
colvarbias *b;
|
|
cvm::real energy_diff = 0.;
|
|
b = bias_by_name(bias_name);
|
|
if (b == NULL) {
|
|
cvm::error("Error: bias not found: " + bias_name);
|
|
return 0.;
|
|
}
|
|
energy_diff = b->energy_difference(conf);
|
|
cvm::decrease_depth();
|
|
return energy_diff;
|
|
}
|
|
|
|
|
|
int colvarmodule::calc()
|
|
{
|
|
int error_code = COLVARS_OK;
|
|
|
|
if (cvm::debug()) {
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Collective variables module, step no. "+
|
|
cvm::to_str(cvm::step_absolute())+"\n");
|
|
}
|
|
|
|
error_code |= calc_colvars();
|
|
error_code |= calc_biases();
|
|
error_code |= update_colvar_forces();
|
|
|
|
error_code |= analyze();
|
|
|
|
// write trajectory files, if needed
|
|
if (cv_traj_freq && cv_traj_name.size()) {
|
|
error_code |= write_traj_files();
|
|
}
|
|
|
|
// write restart files and similar data
|
|
if (restart_out_freq && (cvm::step_relative() > 0) &&
|
|
((cvm::step_absolute() % restart_out_freq) == 0) ) {
|
|
|
|
if (restart_out_name.size()) {
|
|
// Write restart file, if different from main output
|
|
error_code |= write_restart_file(restart_out_name);
|
|
} else {
|
|
error_code |= write_restart_file(output_prefix()+".colvars.state");
|
|
}
|
|
|
|
cvm::increase_depth();
|
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
cvi != colvars.end();
|
|
cvi++) {
|
|
// TODO remove this when corrFunc becomes a bias
|
|
error_code |= (*cvi)->write_output_files();
|
|
}
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
error_code |= (*bi)->write_state_to_replicas();
|
|
}
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
// Write output files for biases, at the specified frequency for each
|
|
cvm::increase_depth();
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
if ((*bi)->output_freq > 0) {
|
|
if ((cvm::step_relative() > 0) &&
|
|
((cvm::step_absolute() % (*bi)->output_freq) == 0) ) {
|
|
error_code |= (*bi)->write_output_files();
|
|
}
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
error_code |= end_of_step();
|
|
|
|
// TODO move this to a base-class proxy method that calls this function
|
|
error_code |= proxy->end_of_step();
|
|
|
|
return error_code;
|
|
}
|
|
|
|
|
|
int colvarmodule::calc_colvars()
|
|
{
|
|
if (cvm::debug())
|
|
cvm::log("Calculating collective variables.\n");
|
|
// calculate collective variables and their gradients
|
|
|
|
// First, we need to decide which biases are awake
|
|
// so they can activate colvars as needed
|
|
std::vector<colvarbias *>::iterator bi;
|
|
for (bi = biases.begin(); bi != biases.end(); bi++) {
|
|
int tsf = (*bi)->get_time_step_factor();
|
|
if (tsf > 0 && (step_absolute() % tsf == 0)) {
|
|
(*bi)->enable(colvardeps::f_cvb_awake);
|
|
} else {
|
|
(*bi)->disable(colvardeps::f_cvb_awake);
|
|
}
|
|
}
|
|
|
|
int error_code = COLVARS_OK;
|
|
std::vector<colvar *>::iterator cvi;
|
|
|
|
// Determine which colvars are active at this iteration
|
|
variables_active()->clear();
|
|
variables_active()->reserve(variables()->size());
|
|
for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
|
|
// Wake up or put to sleep variables
|
|
int tsf = (*cvi)->get_time_step_factor();
|
|
if (tsf > 0 && (step_absolute() % tsf == 0)) {
|
|
(*cvi)->enable(colvardeps::f_cv_awake);
|
|
} else {
|
|
(*cvi)->disable(colvardeps::f_cv_awake);
|
|
}
|
|
|
|
if ((*cvi)->is_enabled()) {
|
|
variables_active()->push_back(*cvi);
|
|
}
|
|
}
|
|
|
|
// if SMP support is available, split up the work
|
|
if (proxy->smp_enabled() == COLVARS_OK) {
|
|
|
|
// first, calculate how much work (currently, how many active CVCs) each colvar has
|
|
|
|
variables_active_smp()->clear();
|
|
variables_active_smp_items()->clear();
|
|
|
|
variables_active_smp()->reserve(variables_active()->size());
|
|
variables_active_smp_items()->reserve(variables_active()->size());
|
|
|
|
// set up a vector containing all components
|
|
cvm::increase_depth();
|
|
for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
|
|
|
|
error_code |= (*cvi)->update_cvc_flags();
|
|
|
|
size_t num_items = (*cvi)->num_active_cvcs();
|
|
variables_active_smp()->reserve(variables_active_smp()->size() + num_items);
|
|
variables_active_smp_items()->reserve(variables_active_smp_items()->size() + num_items);
|
|
for (size_t icvc = 0; icvc < num_items; icvc++) {
|
|
variables_active_smp()->push_back(*cvi);
|
|
variables_active_smp_items()->push_back(icvc);
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
// calculate colvar components in parallel
|
|
error_code |= proxy->smp_colvars_loop();
|
|
|
|
cvm::increase_depth();
|
|
for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
|
|
error_code |= (*cvi)->collect_cvc_data();
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
} else {
|
|
|
|
// calculate colvars one at a time
|
|
cvm::increase_depth();
|
|
for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
|
|
error_code |= (*cvi)->calc();
|
|
if (cvm::get_error()) {
|
|
return COLVARS_ERROR;
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
error_code |= cvm::get_error();
|
|
return error_code;
|
|
}
|
|
|
|
|
|
int colvarmodule::calc_biases()
|
|
{
|
|
// update the biases and communicate their forces to the collective
|
|
// variables
|
|
if (cvm::debug() && num_biases())
|
|
cvm::log("Updating collective variable biases.\n");
|
|
|
|
// set biasing forces to zero before biases are calculated and summed over
|
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
cvi != colvars.end(); cvi++) {
|
|
(*cvi)->reset_bias_force();
|
|
}
|
|
|
|
std::vector<colvarbias *>::iterator bi;
|
|
int error_code = COLVARS_OK;
|
|
|
|
// Total bias energy is reset before calling scripted biases
|
|
total_bias_energy = 0.0;
|
|
|
|
// update the list of active biases
|
|
// which may have changed based on f_cvb_awake in calc_colvars()
|
|
biases_active()->clear();
|
|
biases_active()->reserve(biases.size());
|
|
for (bi = biases.begin(); bi != biases.end(); bi++) {
|
|
if ((*bi)->is_enabled()) {
|
|
biases_active()->push_back(*bi);
|
|
}
|
|
}
|
|
|
|
// if SMP support is available, split up the work
|
|
if (proxy->smp_enabled() == COLVARS_OK) {
|
|
|
|
if (use_scripted_forces && !scripting_after_biases) {
|
|
// calculate biases and scripted forces in parallel
|
|
error_code |= proxy->smp_biases_script_loop();
|
|
} else {
|
|
// calculate biases in parallel
|
|
error_code |= proxy->smp_biases_loop();
|
|
}
|
|
|
|
} else {
|
|
|
|
if (use_scripted_forces && !scripting_after_biases) {
|
|
error_code |= calc_scripted_forces();
|
|
}
|
|
|
|
cvm::increase_depth();
|
|
for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
|
|
error_code |= (*bi)->update();
|
|
if (cvm::get_error()) {
|
|
return error_code;
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
|
|
total_bias_energy += (*bi)->get_energy();
|
|
}
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::update_colvar_forces()
|
|
{
|
|
int error_code = COLVARS_OK;
|
|
|
|
std::vector<colvar *>::iterator cvi;
|
|
std::vector<colvarbias *>::iterator bi;
|
|
|
|
// sum the forces from all biases for each collective variable
|
|
if (cvm::debug() && num_biases())
|
|
cvm::log("Collecting forces from all biases.\n");
|
|
cvm::increase_depth();
|
|
for (bi = biases_active()->begin(); bi != biases_active()->end(); bi++) {
|
|
(*bi)->communicate_forces();
|
|
if (cvm::get_error()) {
|
|
return COLVARS_ERROR;
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
if (use_scripted_forces && scripting_after_biases) {
|
|
error_code |= calc_scripted_forces();
|
|
}
|
|
|
|
// Now we have collected energies from both built-in and scripted biases
|
|
if (cvm::debug())
|
|
cvm::log("Adding total bias energy: " + cvm::to_str(total_bias_energy) + "\n");
|
|
proxy->add_energy(total_bias_energy);
|
|
|
|
cvm::real total_colvar_energy = 0.0;
|
|
// sum up the forces for each colvar, including wall forces
|
|
// and integrate any internal
|
|
// equation of motion (extended system)
|
|
if (cvm::debug())
|
|
cvm::log("Updating the internal degrees of freedom "
|
|
"of colvars (if they have any).\n");
|
|
cvm::increase_depth();
|
|
for (cvi = variables()->begin(); cvi != variables()->end(); cvi++) {
|
|
// Inactive colvars will only reset their forces and return 0 energy
|
|
total_colvar_energy += (*cvi)->update_forces_energy();
|
|
if (cvm::get_error()) {
|
|
return COLVARS_ERROR;
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
if (cvm::debug())
|
|
cvm::log("Adding total colvar energy: " + cvm::to_str(total_colvar_energy) + "\n");
|
|
proxy->add_energy(total_colvar_energy);
|
|
|
|
// make collective variables communicate their forces to their
|
|
// coupled degrees of freedom (i.e. atoms)
|
|
if (cvm::debug())
|
|
cvm::log("Communicating forces from the colvars to the atoms.\n");
|
|
cvm::increase_depth();
|
|
for (cvi = variables_active()->begin(); cvi != variables_active()->end(); cvi++) {
|
|
if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
|
|
(*cvi)->communicate_forces();
|
|
if (cvm::get_error()) {
|
|
return COLVARS_ERROR;
|
|
}
|
|
}
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::calc_scripted_forces()
|
|
{
|
|
// Run user force script, if provided,
|
|
// potentially adding scripted forces to the colvars
|
|
int res;
|
|
res = proxy->run_force_callback();
|
|
if (res == COLVARS_NOT_IMPLEMENTED) {
|
|
cvm::error("Colvar forces scripts are not implemented.");
|
|
return COLVARS_NOT_IMPLEMENTED;
|
|
}
|
|
if (res != COLVARS_OK) {
|
|
cvm::error("Error running user colvar forces script");
|
|
return COLVARS_ERROR;
|
|
}
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int colvarmodule::write_restart_file(std::string const &out_name)
|
|
{
|
|
cvm::log("Saving collective variables state to \""+out_name+"\".\n");
|
|
proxy->backup_file(out_name);
|
|
std::ostream *restart_out_os = proxy->output_stream(out_name);
|
|
if (!restart_out_os) return cvm::get_error();
|
|
if (!write_restart(*restart_out_os)) {
|
|
return cvm::error("Error: in writing restart file.\n", COLVARS_FILE_ERROR);
|
|
}
|
|
proxy->close_output_stream(out_name);
|
|
if (cv_traj_os != NULL) {
|
|
// Take the opportunity to flush colvars.traj
|
|
proxy->flush_output_stream(cv_traj_os);
|
|
}
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::write_restart_string(std::string &output)
|
|
{
|
|
cvm::log("Saving state to output buffer.\n");
|
|
std::ostringstream os;
|
|
if (!write_restart(os)) {
|
|
return cvm::error("Error: in writing restart to buffer.\n", COLVARS_FILE_ERROR);
|
|
}
|
|
output = os.str();
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int colvarmodule::write_traj_files()
|
|
{
|
|
if (cvm::debug()) {
|
|
cvm::log("colvarmodule::write_traj_files()\n");
|
|
}
|
|
|
|
if (cv_traj_os == NULL) {
|
|
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 ||
|
|
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);
|
|
}
|
|
|
|
if (restart_out_freq && (cv_traj_os != NULL) &&
|
|
((cvm::step_absolute() % restart_out_freq) == 0)) {
|
|
cvm::log("Synchronizing (emptying the buffer of) trajectory file \""+
|
|
cv_traj_name+"\".\n");
|
|
proxy->flush_output_stream(cv_traj_os);
|
|
}
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::analyze()
|
|
{
|
|
if (cvm::debug()) {
|
|
cvm::log("colvarmodule::analyze(), step = "+cvm::to_str(it)+".\n");
|
|
}
|
|
|
|
// perform colvar-specific analysis
|
|
for (std::vector<colvar *>::iterator cvi = variables_active()->begin();
|
|
cvi != variables_active()->end();
|
|
cvi++) {
|
|
cvm::increase_depth();
|
|
(*cvi)->analyze();
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
// perform bias-specific analysis
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
cvm::increase_depth();
|
|
(*bi)->analyze();
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::end_of_step()
|
|
{
|
|
if (cvm::debug()) {
|
|
cvm::log("colvarmodule::end_of_step(), step = "+cvm::to_str(it)+".\n");
|
|
}
|
|
|
|
for (std::vector<colvar *>::iterator cvi = variables_active()->begin();
|
|
cvi != variables_active()->end();
|
|
cvi++) {
|
|
cvm::increase_depth();
|
|
(*cvi)->end_of_step();
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
// perform bias-specific analysis
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
cvm::increase_depth();
|
|
(*bi)->end_of_step();
|
|
cvm::decrease_depth();
|
|
}
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::setup()
|
|
{
|
|
if (this->size() == 0) return cvm::get_error();
|
|
for (std::vector<colvar *>::iterator cvi = variables()->begin();
|
|
cvi != variables()->end(); cvi++) {
|
|
(*cvi)->setup();
|
|
}
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
colvarmodule::~colvarmodule()
|
|
{
|
|
if ((proxy->smp_thread_id() == COLVARS_NOT_IMPLEMENTED) ||
|
|
(proxy->smp_thread_id() == 0)) {
|
|
|
|
reset();
|
|
|
|
// Delete contents of static arrays
|
|
colvarbias::delete_features();
|
|
colvar::delete_features();
|
|
colvar::cvc::delete_features();
|
|
atom_group::delete_features();
|
|
|
|
delete
|
|
reinterpret_cast<std::map<std::string, int> *>(num_biases_types_used_);
|
|
num_biases_types_used_ = NULL;
|
|
|
|
delete parse;
|
|
parse = NULL;
|
|
|
|
delete usage_;
|
|
usage_ = NULL;
|
|
|
|
// The proxy object will be deallocated last (if at all)
|
|
proxy = NULL;
|
|
}
|
|
}
|
|
|
|
|
|
int colvarmodule::reset()
|
|
{
|
|
cvm::log("Resetting the Collective Variables module.\n");
|
|
|
|
parse->clear();
|
|
|
|
// Iterate backwards because we are deleting the elements as we go
|
|
for (std::vector<colvarbias *>::reverse_iterator bi = biases.rbegin();
|
|
bi != biases.rend();
|
|
bi++) {
|
|
delete *bi; // the bias destructor updates the biases array
|
|
}
|
|
biases.clear();
|
|
biases_active_.clear();
|
|
|
|
// Reset counters tracking usage of each bias type
|
|
reinterpret_cast<std::map<std::string, int> *>(num_biases_types_used_)->clear();
|
|
|
|
// Iterate backwards because we are deleting the elements as we go
|
|
for (std::vector<colvar *>::reverse_iterator cvi = colvars.rbegin();
|
|
cvi != colvars.rend();
|
|
cvi++) {
|
|
delete *cvi; // the colvar destructor updates the colvars array
|
|
}
|
|
colvars.clear();
|
|
|
|
reset_index_groups();
|
|
|
|
proxy->flush_output_streams();
|
|
proxy->reset();
|
|
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::setup_input()
|
|
{
|
|
if (proxy->input_prefix().size()) {
|
|
// Read a state file
|
|
std::string restart_in_name(proxy->input_prefix()+
|
|
std::string(".colvars.state"));
|
|
std::ifstream input_is(restart_in_name.c_str());
|
|
if (!input_is.good()) {
|
|
// Try without the suffix
|
|
input_is.clear();
|
|
restart_in_name = proxy->input_prefix();
|
|
input_is.open(restart_in_name.c_str());
|
|
}
|
|
|
|
// Now that the file has been opened, clear this for the next round
|
|
proxy->input_prefix().clear();
|
|
|
|
if (!input_is.good()) {
|
|
return cvm::error("Error: in opening input state file \""+
|
|
std::string(restart_in_name)+"\".\n",
|
|
COLVARS_FILE_ERROR);
|
|
} else {
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Loading state from file \""+restart_in_name+"\".\n");
|
|
read_restart(input_is);
|
|
cvm::log(cvm::line_marker);
|
|
return cvm::get_error();
|
|
}
|
|
}
|
|
|
|
if (proxy->input_buffer() != NULL) {
|
|
// Read a string buffer
|
|
char const *buffer = proxy->input_buffer();
|
|
size_t const buffer_size = strlen(proxy->input_buffer());
|
|
// Clear proxy pointer for the next round
|
|
proxy->input_buffer() = NULL;
|
|
if (buffer_size > 0) {
|
|
std::istringstream input_is;
|
|
// Replace the buffer of input_is; work around the lack of const in
|
|
// pubsetbuf's prototype (which also needs to support output streams)
|
|
input_is.rdbuf()->pubsetbuf(const_cast<char *>(buffer), buffer_size);
|
|
cvm::log(cvm::line_marker);
|
|
cvm::log("Loading state from input buffer.\n");
|
|
read_restart(input_is);
|
|
cvm::log(cvm::line_marker);
|
|
return cvm::get_error();
|
|
}
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int colvarmodule::setup_output()
|
|
{
|
|
int error_code = COLVARS_OK;
|
|
|
|
// output state file (restart)
|
|
restart_out_name = proxy->restart_output_prefix().size() ?
|
|
std::string(proxy->restart_output_prefix()+".colvars.state") :
|
|
std::string("");
|
|
|
|
if (restart_out_name.size()) {
|
|
cvm::log("The restart output state file will be \""+
|
|
restart_out_name+"\".\n");
|
|
}
|
|
|
|
output_prefix() = proxy->output_prefix();
|
|
if (output_prefix().size()) {
|
|
cvm::log("The final output state file will be \""+
|
|
(output_prefix().size() ?
|
|
std::string(output_prefix()+".colvars.state") :
|
|
std::string("colvars.state"))+"\".\n");
|
|
// cvm::log (cvm::line_marker);
|
|
}
|
|
|
|
cv_traj_name =
|
|
(output_prefix().size() ?
|
|
std::string(output_prefix()+".colvars.traj") :
|
|
std::string(""));
|
|
|
|
if (cv_traj_freq && cv_traj_name.size()) {
|
|
error_code |= open_traj_file(cv_traj_name);
|
|
}
|
|
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
error_code |= (*bi)->setup_output();
|
|
}
|
|
|
|
if (error_code != COLVARS_OK || cvm::get_error()) {
|
|
set_error_bits(COLVARS_FILE_ERROR);
|
|
}
|
|
|
|
return cvm::get_error();
|
|
}
|
|
|
|
|
|
std::string colvarmodule::state_file_prefix(char const *filename)
|
|
{
|
|
std::string const filename_str(filename);
|
|
std::string const prefix =
|
|
filename_str.substr(0, filename_str.find(".colvars.state"));
|
|
if (prefix.size() == 0) {
|
|
cvm::error("Error: invalid filename/prefix value \""+filename_str+"\".",
|
|
COLVARS_INPUT_ERROR);
|
|
}
|
|
return prefix;
|
|
}
|
|
|
|
|
|
|
|
std::istream & colvarmodule::read_restart(std::istream &is)
|
|
{
|
|
bool warn_total_forces = false;
|
|
|
|
{
|
|
// read global restart information
|
|
std::string restart_conf;
|
|
if (is >> colvarparse::read_block("configuration", &restart_conf)) {
|
|
|
|
parse->get_keyval(restart_conf, "step",
|
|
it_restart, static_cast<step_number>(0),
|
|
colvarparse::parse_restart);
|
|
it = it_restart;
|
|
|
|
restart_version_str.clear();
|
|
restart_version_int = 0;
|
|
parse->get_keyval(restart_conf, "version",
|
|
restart_version_str, std::string(""),
|
|
colvarparse::parse_restart);
|
|
if (restart_version_str.size()) {
|
|
// Initialize integer version number of this restart file
|
|
restart_version_int =
|
|
proxy->get_version_from_string(restart_version_str.c_str());
|
|
}
|
|
|
|
if (restart_version() != version()) {
|
|
cvm::log("This state file was generated with version "+
|
|
restart_version()+"\n");
|
|
}
|
|
|
|
if (restart_version_number() < 20160810) {
|
|
// check for total force change
|
|
if (proxy->total_forces_enabled()) {
|
|
warn_total_forces = true;
|
|
}
|
|
}
|
|
|
|
std::string units_restart;
|
|
if (parse->get_keyval(restart_conf, "units",
|
|
units_restart, std::string(""),
|
|
colvarparse::parse_restart)) {
|
|
units_restart = colvarparse::to_lower_cppstr(units_restart);
|
|
if ((proxy->units.size() > 0) && (units_restart != proxy->units)) {
|
|
cvm::error("Error: the state file has units \""+units_restart+
|
|
"\", but the current unit system is \""+proxy->units+
|
|
"\".\n", COLVARS_INPUT_ERROR);
|
|
}
|
|
}
|
|
|
|
}
|
|
is.clear();
|
|
parse->clear_keyword_registry();
|
|
}
|
|
|
|
print_total_forces_errning(warn_total_forces);
|
|
|
|
read_objects_state(is);
|
|
|
|
return is;
|
|
}
|
|
|
|
|
|
|
|
std::istream & colvarmodule::read_objects_state(std::istream &is)
|
|
{
|
|
std::streampos 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",
|
|
COLVARS_INPUT_ERROR);
|
|
}
|
|
if (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",
|
|
COLVARS_INPUT_ERROR);
|
|
}
|
|
if (is.tellg() > pos) break; // found it
|
|
}
|
|
cvm::decrease_depth();
|
|
}
|
|
}
|
|
|
|
if (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;
|
|
}
|
|
|
|
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");
|
|
cvm::log(" https://colvars.github.io/README-totalforce.html\n");
|
|
// update this ahead of time in this special case
|
|
output_prefix() = proxy->input_prefix();
|
|
cvm::log("All output files will now be saved with the prefix \""+output_prefix()+".tmp.*\".\n");
|
|
cvm::log("Please review the important warning above. After that, you may rename:\n\
|
|
\""+output_prefix()+".tmp.colvars.state\"\n\
|
|
to:\n\
|
|
\""+proxy->input_prefix()+".colvars.state\"\n\
|
|
and load it to continue this simulation.\n");
|
|
output_prefix() = output_prefix()+".tmp";
|
|
write_restart_file(output_prefix()+".colvars.state");
|
|
return cvm::error("Exiting with error until issue is addressed.\n",
|
|
COLVARS_INPUT_ERROR);
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int colvarmodule::backup_file(char const *filename)
|
|
{
|
|
return proxy->backup_file(filename);
|
|
}
|
|
|
|
|
|
int colvarmodule::write_output_files()
|
|
{
|
|
int error_code = COLVARS_OK;
|
|
cvm::increase_depth();
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
// Only write output files if they have not already been written this time step
|
|
if ((*bi)->output_freq == 0 ||
|
|
cvm::step_relative() == 0 ||
|
|
(cvm::step_absolute() % (*bi)->output_freq) != 0) {
|
|
error_code |= (*bi)->write_output_files();
|
|
}
|
|
error_code |= (*bi)->write_state_to_replicas();
|
|
}
|
|
cvm::decrease_depth();
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
int colvarmodule::read_traj(char const *traj_filename,
|
|
long traj_read_begin,
|
|
long traj_read_end)
|
|
{
|
|
cvm::log("Opening trajectory file \""+
|
|
std::string(traj_filename)+"\".\n");
|
|
std::ifstream traj_is(traj_filename);
|
|
|
|
while (true) {
|
|
while (true) {
|
|
|
|
std::string line("");
|
|
|
|
do {
|
|
if (!colvarparse::getline_nocomments(traj_is, line)) {
|
|
cvm::log("End of file \""+std::string(traj_filename)+
|
|
"\" reached, or corrupted file.\n");
|
|
traj_is.close();
|
|
return false;
|
|
}
|
|
} while (line.find_first_not_of(colvarparse::white_space) == std::string::npos);
|
|
|
|
std::istringstream is(line);
|
|
|
|
if (!(is >> it)) return false;
|
|
|
|
if ( (it < traj_read_begin) ) {
|
|
|
|
if ((it % 1000) == 0)
|
|
std::cerr << "Skipping trajectory step " << it
|
|
<< " \r";
|
|
|
|
continue;
|
|
|
|
} else {
|
|
|
|
if ((it % 1000) == 0)
|
|
std::cerr << "Reading from trajectory, step = " << it
|
|
<< " \r";
|
|
|
|
if ( (traj_read_end > traj_read_begin) &&
|
|
(it > traj_read_end) ) {
|
|
std::cerr << "\n";
|
|
cvm::error("Reached the end of the trajectory, "
|
|
"read_end = "+cvm::to_str(traj_read_end)+"\n",
|
|
COLVARS_FILE_ERROR);
|
|
return COLVARS_ERROR;
|
|
}
|
|
|
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
cvi != colvars.end();
|
|
cvi++) {
|
|
if (!(*cvi)->read_traj(is)) {
|
|
cvm::error("Error: in reading colvar \""+(*cvi)->name+
|
|
"\" from trajectory file \""+
|
|
std::string(traj_filename)+"\".\n",
|
|
COLVARS_FILE_ERROR);
|
|
return COLVARS_ERROR;
|
|
}
|
|
}
|
|
|
|
break;
|
|
}
|
|
}
|
|
}
|
|
return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
|
|
}
|
|
|
|
|
|
std::ostream & colvarmodule::write_restart(std::ostream &os)
|
|
{
|
|
os.setf(std::ios::scientific, std::ios::floatfield);
|
|
os << "configuration {\n"
|
|
<< " step " << std::setw(it_width)
|
|
<< it << "\n"
|
|
<< " dt " << dt() << "\n"
|
|
<< " version " << std::string(COLVARS_VERSION) << "\n";
|
|
if (proxy->units.size() > 0) {
|
|
os << " units " << proxy->units << "\n";
|
|
}
|
|
os << "}\n\n";
|
|
|
|
int error_code = COLVARS_OK;
|
|
|
|
cvm::increase_depth();
|
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
cvi != colvars.end();
|
|
cvi++) {
|
|
(*cvi)->write_state(os);
|
|
}
|
|
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
(*bi)->write_state(os);
|
|
}
|
|
cvm::decrease_depth();
|
|
|
|
if (error_code != COLVARS_OK) {
|
|
// TODO make this function return an int instead
|
|
os.setstate(std::ios::failbit);
|
|
}
|
|
|
|
return os;
|
|
}
|
|
|
|
|
|
int colvarmodule::open_traj_file(std::string const &file_name)
|
|
{
|
|
if (cv_traj_os != NULL) {
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
// (re)open trajectory file
|
|
if (cv_traj_append) {
|
|
cvm::log("Appending to trajectory file \""+file_name+"\".\n");
|
|
cv_traj_os = (cvm::proxy)->output_stream(file_name, std::ios::app);
|
|
} else {
|
|
cvm::log("Opening trajectory file \""+file_name+"\".\n");
|
|
proxy->backup_file(file_name.c_str());
|
|
cv_traj_os = (cvm::proxy)->output_stream(file_name);
|
|
}
|
|
|
|
if (cv_traj_os == NULL) {
|
|
cvm::error("Error: cannot write to file \""+file_name+"\".\n",
|
|
COLVARS_FILE_ERROR);
|
|
}
|
|
|
|
return cvm::get_error();
|
|
}
|
|
|
|
|
|
int colvarmodule::close_traj_file()
|
|
{
|
|
if (cv_traj_os != NULL) {
|
|
cvm::log("Closing trajectory file \""+cv_traj_name+"\".\n");
|
|
proxy->close_output_stream(cv_traj_name);
|
|
cv_traj_os = NULL;
|
|
}
|
|
return cvm::get_error();
|
|
}
|
|
|
|
|
|
std::ostream & colvarmodule::write_traj_label(std::ostream &os)
|
|
{
|
|
os.setf(std::ios::scientific, std::ios::floatfield);
|
|
|
|
os << "# " << cvm::wrap_string("step", cvm::it_width-2)
|
|
<< " ";
|
|
|
|
cvm::increase_depth();
|
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
cvi != colvars.end();
|
|
cvi++) {
|
|
(*cvi)->write_traj_label(os);
|
|
}
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
(*bi)->write_traj_label(os);
|
|
}
|
|
os << "\n";
|
|
|
|
if (cvm::debug()) {
|
|
proxy->flush_output_stream(&os);
|
|
}
|
|
|
|
cvm::decrease_depth();
|
|
return os;
|
|
}
|
|
|
|
|
|
std::ostream & colvarmodule::write_traj(std::ostream &os)
|
|
{
|
|
os.setf(std::ios::scientific, std::ios::floatfield);
|
|
|
|
os << std::setw(cvm::it_width) << it
|
|
<< " ";
|
|
|
|
cvm::increase_depth();
|
|
for (std::vector<colvar *>::iterator cvi = colvars.begin();
|
|
cvi != colvars.end();
|
|
cvi++) {
|
|
(*cvi)->write_traj(os);
|
|
}
|
|
for (std::vector<colvarbias *>::iterator bi = biases.begin();
|
|
bi != biases.end();
|
|
bi++) {
|
|
(*bi)->write_traj(os);
|
|
}
|
|
os << "\n";
|
|
|
|
if (cvm::debug()) {
|
|
proxy->flush_output_stream(&os);
|
|
}
|
|
|
|
cvm::decrease_depth();
|
|
return os;
|
|
}
|
|
|
|
|
|
void colvarmodule::log(std::string const &message, int min_log_level)
|
|
{
|
|
if (cvm::log_level() < min_log_level) return;
|
|
// allow logging when the module is not fully initialized
|
|
size_t const d = (cvm::main() != NULL) ? depth() : 0;
|
|
if (d > 0) {
|
|
proxy->log((std::string(2*d, ' '))+message);
|
|
} else {
|
|
proxy->log(message);
|
|
}
|
|
}
|
|
|
|
|
|
void colvarmodule::increase_depth()
|
|
{
|
|
(depth())++;
|
|
}
|
|
|
|
|
|
void colvarmodule::decrease_depth()
|
|
{
|
|
if (depth() > 0) {
|
|
(depth())--;
|
|
}
|
|
}
|
|
|
|
|
|
size_t & colvarmodule::depth()
|
|
{
|
|
// NOTE: do not call log() or error() here, to avoid recursion
|
|
colvarmodule *cv = cvm::main();
|
|
if (proxy->smp_enabled() == COLVARS_OK) {
|
|
int const nt = proxy->smp_num_threads();
|
|
if (int(cv->depth_v.size()) != nt) {
|
|
proxy->smp_lock();
|
|
// update array of depths
|
|
if (cv->depth_v.size() > 0) { cv->depth_s = cv->depth_v[0]; }
|
|
cv->depth_v.clear();
|
|
cv->depth_v.assign(nt, cv->depth_s);
|
|
proxy->smp_unlock();
|
|
}
|
|
return cv->depth_v[proxy->smp_thread_id()];
|
|
}
|
|
return cv->depth_s;
|
|
}
|
|
|
|
|
|
void colvarmodule::set_error_bits(int code)
|
|
{
|
|
if (code < 0) {
|
|
cvm::log("Error: set_error_bits() received negative error code.\n");
|
|
return;
|
|
}
|
|
proxy->smp_lock();
|
|
errorCode |= code | COLVARS_ERROR;
|
|
proxy->smp_unlock();
|
|
}
|
|
|
|
|
|
bool colvarmodule::get_error_bit(int code)
|
|
{
|
|
return bool(errorCode & code);
|
|
}
|
|
|
|
|
|
void colvarmodule::clear_error()
|
|
{
|
|
proxy->smp_lock();
|
|
errorCode = COLVARS_OK;
|
|
proxy->smp_unlock();
|
|
proxy->clear_error_msgs();
|
|
}
|
|
|
|
|
|
int colvarmodule::error(std::string const &message, int code)
|
|
{
|
|
set_error_bits(code);
|
|
proxy->error(message);
|
|
return get_error();
|
|
}
|
|
|
|
|
|
int cvm::read_index_file(char const *filename)
|
|
{
|
|
std::ifstream is(filename, std::ios::binary);
|
|
if (!is.good()) {
|
|
return cvm::error("Error: in opening index file \""+
|
|
std::string(filename)+"\".\n",
|
|
COLVARS_FILE_ERROR);
|
|
} else {
|
|
index_file_names.push_back(std::string(filename));
|
|
}
|
|
|
|
while (is.good()) {
|
|
char open, close;
|
|
std::string group_name;
|
|
int index_of_group = -1;
|
|
if ( (is >> open) && (open == '[') &&
|
|
(is >> group_name) &&
|
|
(is >> close) && (close == ']') ) {
|
|
size_t i = 0;
|
|
for ( ; i < index_group_names.size(); i++) {
|
|
if (index_group_names[i] == group_name) {
|
|
// Found a group with the same name
|
|
index_of_group = i;
|
|
}
|
|
}
|
|
if (index_of_group < 0) {
|
|
index_group_names.push_back(group_name);
|
|
index_groups.push_back(NULL);
|
|
index_of_group = index_groups.size()-1;
|
|
}
|
|
} else {
|
|
return cvm::error("Error: in parsing index file \""+
|
|
std::string(filename)+"\".\n",
|
|
COLVARS_INPUT_ERROR);
|
|
}
|
|
|
|
std::vector<int> *old_index_group = index_groups[index_of_group];
|
|
std::vector<int> *new_index_group = new std::vector<int>();
|
|
|
|
int atom_number = 1;
|
|
std::streampos pos = is.tellg();
|
|
while ( (is >> atom_number) && (atom_number > 0) ) {
|
|
new_index_group->push_back(atom_number);
|
|
pos = is.tellg();
|
|
}
|
|
|
|
if (old_index_group != NULL) {
|
|
bool equal = false;
|
|
if (new_index_group->size() == old_index_group->size()) {
|
|
if (std::equal(new_index_group->begin(), new_index_group->end(),
|
|
old_index_group->begin())) {
|
|
equal = true;
|
|
}
|
|
}
|
|
if (! equal) {
|
|
new_index_group->clear();
|
|
delete new_index_group;
|
|
new_index_group = NULL;
|
|
return cvm::error("Error: the index group \""+group_name+
|
|
"\" was redefined.\n", COLVARS_INPUT_ERROR);
|
|
} else {
|
|
old_index_group->clear();
|
|
delete old_index_group;
|
|
old_index_group = NULL;
|
|
}
|
|
}
|
|
|
|
index_groups[index_of_group] = new_index_group;
|
|
|
|
is.clear();
|
|
is.seekg(pos, std::ios::beg);
|
|
std::string delim;
|
|
if ( (is >> delim) && (delim == "[") ) {
|
|
// new group
|
|
is.clear();
|
|
is.seekg(pos, std::ios::beg);
|
|
} else {
|
|
break;
|
|
}
|
|
}
|
|
|
|
cvm::log("The following index groups are currently defined:\n");
|
|
size_t i = 0;
|
|
for ( ; i < index_group_names.size(); i++) {
|
|
cvm::log(" "+(index_group_names[i])+" ("+
|
|
cvm::to_str((index_groups[i])->size())+" atoms)\n");
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int colvarmodule::reset_index_groups()
|
|
{
|
|
size_t i = 0;
|
|
for ( ; i < index_groups.size(); i++) {
|
|
delete index_groups[i];
|
|
index_groups[i] = NULL;
|
|
}
|
|
index_group_names.clear();
|
|
index_groups.clear();
|
|
index_file_names.clear();
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
int cvm::load_atoms(char const *file_name,
|
|
cvm::atom_group &atoms,
|
|
std::string const &pdb_field,
|
|
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::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) {
|
|
return cvm::error("Error: PDB column may not be specified "
|
|
"for XYZ coordinate files.\n", COLVARS_INPUT_ERROR);
|
|
}
|
|
// For XYZ files, use internal parser
|
|
error_code |= cvm::main()->load_coords_xyz(file_name, &sorted_pos, atoms);
|
|
} else {
|
|
// 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<rvector> *pos,
|
|
cvm::atom_group *atoms)
|
|
{
|
|
std::ifstream xyz_is(filename);
|
|
unsigned int natoms;
|
|
char symbol[256];
|
|
std::string line;
|
|
cvm::real x = 0.0, y = 0.0, z = 0.0;
|
|
|
|
std::string const error_msg("Error: cannot parse XYZ file \""+
|
|
std::string(filename)+"\".\n");
|
|
|
|
if ( ! (xyz_is >> natoms) ) {
|
|
return cvm::error(error_msg, COLVARS_INPUT_ERROR);
|
|
}
|
|
|
|
++xyz_reader_use_count;
|
|
if (xyz_reader_use_count < 2) {
|
|
cvm::log("Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units.\n");
|
|
}
|
|
|
|
if (xyz_is.good()) {
|
|
// skip comment line
|
|
cvm::getline(xyz_is, line);
|
|
cvm::getline(xyz_is, line);
|
|
xyz_is.width(255);
|
|
} else {
|
|
return cvm::error(error_msg, COLVARS_INPUT_ERROR);
|
|
}
|
|
|
|
std::vector<atom_pos>::iterator pos_i = pos->begin();
|
|
size_t xyz_natoms = 0;
|
|
if (pos->size() != natoms) { // Use specified indices
|
|
int next = 0; // indices are zero-based
|
|
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);
|
|
next++;
|
|
}
|
|
if (xyz_is.good()) {
|
|
xyz_is >> symbol;
|
|
xyz_is >> x >> y >> z;
|
|
// XYZ files are assumed to be in Angstrom (as eg. VMD will)
|
|
(*pos_i)[0] = proxy->angstrom_to_internal(x);
|
|
(*pos_i)[1] = proxy->angstrom_to_internal(y);
|
|
(*pos_i)[2] = proxy->angstrom_to_internal(z);
|
|
xyz_natoms++;
|
|
} else {
|
|
return cvm::error(error_msg, COLVARS_INPUT_ERROR);
|
|
}
|
|
}
|
|
|
|
} else { // Use all positions
|
|
|
|
for ( ; pos_i != pos->end() ; pos_i++) {
|
|
if (xyz_is.good()) {
|
|
xyz_is >> symbol;
|
|
xyz_is >> x >> y >> z;
|
|
(*pos_i)[0] = proxy->angstrom_to_internal(x);
|
|
(*pos_i)[1] = proxy->angstrom_to_internal(y);
|
|
(*pos_i)[2] = proxy->angstrom_to_internal(z);
|
|
xyz_natoms++;
|
|
} else {
|
|
return cvm::error(error_msg, COLVARS_INPUT_ERROR);
|
|
}
|
|
}
|
|
}
|
|
|
|
if (xyz_natoms != pos->size()) {
|
|
return cvm::error("Error: The number of positions read from file \""+
|
|
std::string(filename)+"\" does not match the number of "+
|
|
"positions required: "+cvm::to_str(xyz_natoms)+" vs. "+
|
|
cvm::to_str(pos->size())+".\n", COLVARS_INPUT_ERROR);
|
|
}
|
|
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
|
|
// Wrappers to proxy functions: these may go in the future
|
|
|
|
|
|
cvm::real cvm::boltzmann()
|
|
{
|
|
return proxy->boltzmann();
|
|
}
|
|
|
|
|
|
cvm::real cvm::temperature()
|
|
{
|
|
return proxy->temperature();
|
|
}
|
|
|
|
|
|
cvm::real cvm::dt()
|
|
{
|
|
return proxy->dt();
|
|
}
|
|
|
|
|
|
void cvm::request_total_force()
|
|
{
|
|
proxy->request_total_force(true);
|
|
}
|
|
|
|
|
|
cvm::rvector cvm::position_distance(cvm::atom_pos const &pos1,
|
|
cvm::atom_pos const &pos2)
|
|
{
|
|
return proxy->position_distance(pos1, pos2);
|
|
}
|
|
|
|
|
|
cvm::real cvm::rand_gaussian(void)
|
|
{
|
|
return proxy->rand_gaussian();
|
|
}
|
|
|
|
|
|
template<typename T> std::string _to_str(T const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
std::ostringstream os;
|
|
if (width) os.width(width);
|
|
if (prec) {
|
|
os.setf(std::ios::scientific, std::ios::floatfield);
|
|
os.precision(prec);
|
|
}
|
|
os << x;
|
|
return os.str();
|
|
}
|
|
|
|
|
|
template<typename T> std::string _to_str_vector(std::vector<T> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
if (!x.size()) return std::string("");
|
|
std::ostringstream os;
|
|
if (prec) {
|
|
os.setf(std::ios::scientific, std::ios::floatfield);
|
|
}
|
|
os << "{ ";
|
|
if (width) os.width(width);
|
|
if (prec) os.precision(prec);
|
|
os << x[0];
|
|
for (size_t i = 1; i < x.size(); i++) {
|
|
os << ", ";
|
|
if (width) os.width(width);
|
|
if (prec) os.precision(prec);
|
|
os << x[i];
|
|
}
|
|
os << " }";
|
|
return os.str();
|
|
}
|
|
|
|
|
|
|
|
std::string colvarmodule::to_str(std::string const &x)
|
|
{
|
|
return std::string("\"")+x+std::string("\"");
|
|
}
|
|
|
|
std::string colvarmodule::to_str(char const *x)
|
|
{
|
|
return std::string("\"")+std::string(x)+std::string("\"");
|
|
}
|
|
|
|
std::string colvarmodule::to_str(bool x)
|
|
{
|
|
return (x ? "on" : "off");
|
|
}
|
|
|
|
std::string colvarmodule::to_str(int const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<int>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(size_t const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<size_t>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(long int const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<long int>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(step_number const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<step_number>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(cvm::real const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<cvm::real>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(cvm::rvector const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<cvm::rvector>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(cvm::quaternion const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<cvm::quaternion>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(colvarvalue const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str<colvarvalue>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(cvm::vector1d<cvm::real> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str< cvm::vector1d<cvm::real> >(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(cvm::matrix2d<cvm::real> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str< cvm::matrix2d<cvm::real> >(x, width, prec);
|
|
}
|
|
|
|
|
|
std::string colvarmodule::to_str(std::vector<int> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<int>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<size_t> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<size_t>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<long int> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<long int>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<cvm::real> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<cvm::real>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<cvm::rvector> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<cvm::rvector>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<cvm::quaternion> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<cvm::quaternion>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<colvarvalue> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<colvarvalue>(x, width, prec);
|
|
}
|
|
|
|
std::string colvarmodule::to_str(std::vector<std::string> const &x,
|
|
size_t width, size_t prec)
|
|
{
|
|
return _to_str_vector<std::string>(x, width, prec);
|
|
}
|
|
|
|
|
|
std::string cvm::wrap_string(std::string const &s, size_t nchars)
|
|
{
|
|
if (!s.size()) {
|
|
return std::string(nchars, ' ');
|
|
} else {
|
|
return ( (s.size() <= nchars) ?
|
|
(s+std::string(nchars-s.size(), ' ')) :
|
|
(std::string(s, 0, nchars)) );
|
|
}
|
|
}
|
|
|
|
|
|
|
|
int colvarmodule::cite_feature(std::string const &feature)
|
|
{
|
|
return usage_->cite_feature(feature);
|
|
}
|
|
|
|
std::string colvarmodule::feature_report(int flag)
|
|
{
|
|
return usage_->report(flag);
|
|
}
|
|
|
|
|
|
colvarmodule::usage::usage()
|
|
{
|
|
#include "colvarmodule_refs.h"
|
|
}
|
|
|
|
int colvarmodule::usage::cite_feature(std::string const &feature)
|
|
{
|
|
if (feature_count_.count(feature) > 0) {
|
|
feature_count_[feature] += 1;
|
|
return cite_paper(feature_paper_map_[feature]);
|
|
}
|
|
cvm::log("Warning: cannot cite unknown feature \""+feature+"\"\n");
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
int colvarmodule::usage::cite_paper(std::string const &paper)
|
|
{
|
|
if (paper_count_.count(paper) > 0) {
|
|
paper_count_[paper] += 1;
|
|
return COLVARS_OK;
|
|
}
|
|
cvm::log("Warning: cannot cite unknown paper \""+paper+"\"\n");
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
std::string colvarmodule::usage::report(int flag)
|
|
{
|
|
std::string result;
|
|
if (flag == 0) {
|
|
// Text
|
|
result += "SUMMARY OF COLVARS FEATURES USED SO FAR AND THEIR CITATIONS:\n";
|
|
}
|
|
if (flag == 1) {
|
|
// LAMMPS log friendly (one-line summary, lowercase message)
|
|
result += "Colvars module (Fiorin2013, plus other works listed for specific features)\n\n";
|
|
}
|
|
|
|
std::map<std::string, int>::iterator p_iter = paper_count_.begin();
|
|
for ( ; p_iter != paper_count_.end(); p_iter++) {
|
|
std::string const paper = p_iter->first;
|
|
int const count = p_iter->second;
|
|
if (count > 0) {
|
|
result += "\n";
|
|
std::map<std::string, std::string>::iterator f_iter =
|
|
feature_paper_map_.begin();
|
|
for ( ; f_iter != feature_paper_map_.end(); f_iter++) {
|
|
if ((f_iter->second == paper) &&
|
|
(feature_count_[f_iter->first] > 0)) {
|
|
if (flag == 0) {
|
|
// URL
|
|
result += "- " + f_iter->first + ":\n";
|
|
}
|
|
if (flag == 1) {
|
|
// BibTeX
|
|
result += "% " + f_iter->first + ":\n";
|
|
}
|
|
}
|
|
}
|
|
if (flag == 0) {
|
|
result += " " + paper + " " + paper_url_[paper] + "\n";
|
|
}
|
|
if (flag == 1) {
|
|
result += paper_bibtex_[paper] + "\n";
|
|
}
|
|
}
|
|
}
|
|
|
|
return result;
|
|
}
|
|
|
|
|
|
// shared pointer to the proxy object
|
|
colvarproxy *colvarmodule::proxy = NULL;
|
|
|
|
// static runtime data
|
|
cvm::real colvarmodule::debug_gradients_step_size = 1.0e-07;
|
|
int colvarmodule::errorCode = 0;
|
|
int colvarmodule::log_level_ = 10;
|
|
cvm::step_number colvarmodule::it = 0;
|
|
cvm::step_number colvarmodule::it_restart = 0;
|
|
size_t colvarmodule::restart_out_freq = 0;
|
|
size_t colvarmodule::cv_traj_freq = 0;
|
|
bool colvarmodule::use_scripted_forces = false;
|
|
bool colvarmodule::scripting_after_biases = true;
|
|
|
|
// i/o constants
|
|
size_t const colvarmodule::it_width = 12;
|
|
size_t const colvarmodule::cv_prec = 14;
|
|
size_t const colvarmodule::cv_width = 21;
|
|
size_t const colvarmodule::en_prec = 14;
|
|
size_t const colvarmodule::en_width = 21;
|
|
const char * const colvarmodule::line_marker = (const char *)
|
|
"----------------------------------------------------------------------\n";
|