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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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62
lib/colvars/colvarbias_alb.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 <stdio.h>
#include <stdlib.h>
#include <math.h>
@ -33,6 +40,9 @@ int colvarbias_alb::init(std::string const &conf)
{
colvarbias::init(conf);
provide(f_cvb_scalar_variables);
enable(f_cvb_scalar_variables);
provide(f_cvb_history_dependent);
size_t i;
@ -239,37 +249,8 @@ int colvarbias_alb::update()
}
std::istream & colvarbias_alb::read_restart(std::istream &is)
int colvarbias_alb::set_state_params(std::string const &conf)
{
size_t const start_pos = is.tellg();
cvm::log("Restarting adaptive linear bias \""+
this->name+"\".\n");
std::string key, brace, conf;
if ( !(is >> key) || !(key == "ALB") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block("configuration", conf)) ) {
cvm::log("Error: in reading restart configuration for restraint 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::fatal_error("Error: in the restart file, the "
"\"ALB\" block has a wrong name\n");
if (name.size() == 0) {
cvm::fatal_error("Error: \"ALB\" block in the restart file "
"has no identifiers.\n");
}
if (!get_keyval(conf, "setCoupling", set_coupling))
cvm::fatal_error("Error: current setCoupling is missing from the restart.\n");
@ -299,23 +280,13 @@ std::istream & colvarbias_alb::read_restart(std::istream &is)
if (!get_keyval(conf, "b_equilibration", b_equilibration))
cvm::fatal_error("Error: current updateCalls is missing from the restart.\n");
is >> brace;
if (brace != "}") {
cvm::fatal_error("Error: corrupt restart information for adaptive linear 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;
return COLVARS_OK;
}
std::ostream & colvarbias_alb::write_restart(std::ostream &os)
std::string const colvarbias_alb::get_state_params() const
{
os << "ALB {\n"
<< " configuration {\n"
<< " name " << this->name << "\n";
std::ostringstream os;
os << " setCoupling ";
size_t i;
for (i = 0; i < colvars.size(); i++) {
@ -358,10 +329,7 @@ std::ostream & colvarbias_alb::write_restart(std::ostream &os)
else
os << " b_equilibration no\n";
os << " }\n"
<< "}\n\n";
return os;
return os.str();
}