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Update Colvars library to version 2016-12-22

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Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
This commit is contained in:
Giacomo Fiorin
2016-12-27 13:17:34 -05:00
parent 6ab716164b
commit f553e230db
49 changed files with 2489 additions and 1358 deletions
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101
lib/colvars/colvarbias_abf.cpp
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@ -1,5 +1,12 @@
// -*- 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 "colvarmodule.h"
#include "colvar.h"
#include "colvarbias_abf.h"
@ -23,6 +30,8 @@ int colvarbias_abf::init(std::string const &conf)
{
colvarbias::init(conf);
provide(f_cvb_scalar_variables);
enable(f_cvb_scalar_variables);
provide(f_cvb_history_dependent);
// TODO relax this in case of VMD plugin
@ -590,16 +599,10 @@ void colvarbias_abf::read_gradients_samples()
}
std::ostream & colvarbias_abf::write_restart(std::ostream& os)
std::ostream & colvarbias_abf::write_state_data(std::ostream& os)
{
std::ios::fmtflags flags(os.flags());
os << "abf {\n"
<< " configuration {\n"
<< " name " << this->name << "\n";
os << " }\n";
os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
os << "\nsamples\n";
samples->write_raw(os, 8);
@ -617,117 +620,47 @@ std::ostream & colvarbias_abf::write_restart(std::ostream& os)
z_gradients->write_raw(os, 8);
}
os << "}\n\n";
os.flags(flags);
return os;
}
std::istream & colvarbias_abf::read_restart(std::istream& is)
std::istream & colvarbias_abf::read_state_data(std::istream& is)
{
if ( input_prefix.size() > 0 ) {
cvm::error("ERROR: cannot provide both inputPrefix and a colvars state file.\n", INPUT_ERROR);
}
size_t const start_pos = is.tellg();
cvm::log("Restarting ABF bias \""+
this->name+"\".\n");
std::string key, brace, conf;
if ( !(is >> key) || !(key == "abf") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block("configuration", conf)) ) {
cvm::log("Error: in reading restart configuration for ABF bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
std::string name = "";
if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::error("Error: in the restart file, the "
"\"abf\" block has wrong name(" + name + ")\n");
if ( name == "" ) {
cvm::error("Error: \"abf\" block in the restart file has no name.\n");
}
if ( !(is >> key) || !(key == "samples")) {
cvm::log("Error: in reading restart configuration for ABF bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
if (! read_state_data_key(is, "samples")) {
return is;
}
if (! samples->read_raw(is)) {
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if ( !(is >> key) || !(key == "gradient")) {
cvm::log("Error: in reading restart configuration for ABF bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
if (! read_state_data_key(is, "gradient")) {
return is;
}
if (! gradients->read_raw(is)) {
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if (z_gradients) {
if ( !(is >> key) || !(key == "z_samples")) {
cvm::log("Error: in reading restart configuration for ABF bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
if (! read_state_data_key(is, "z_samples")) {
return is;
}
if (! z_samples->read_raw(is)) {
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if ( !(is >> key) || !(key == "z_gradient")) {
cvm::log("Error: in reading restart configuration for ABF bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
if (! read_state_data_key(is, "z_gradient")) {
return is;
}
if (! z_gradients->read_raw(is)) {
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
}
is >> brace;
if (brace != "}") {
cvm::error("Error: corrupt restart information for ABF bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str(is.tellg())+" in the restart file.\n");
is.setstate(std::ios::failbit);
}
return is;
}