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Update Colvars to version 2017-07-15 and support automated builds for it

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This commit is contained in:
Giacomo Fiorin
2017-07-19 14:10:43 -04:00
parent cc9b3864bf
commit ee6cac826e
52 changed files with 3473 additions and 2413 deletions
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54
lib/colvars/colvarbias_restraint.cpp
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@ -853,6 +853,21 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
get_keyval(conf, "upperWallConstant", upper_wall_k,
(upper_wall_k > 0.0) ? upper_wall_k : force_k);
if (lower_wall_k * upper_wall_k > 0.0) {
for (size_t i = 0; i < num_variables(); i++) {
if (variables(i)->width != 1.0)
cvm::log("The lower and upper wall force constants for colvar \""+
variables(i)->name+
"\" will be rescaled to "+
cvm::to_str(lower_wall_k /
(variables(i)->width * variables(i)->width))+
" and "+
cvm::to_str(upper_wall_k /
(variables(i)->width * variables(i)->width))+
" according to the specified width.\n");
}
}
enable(f_cvb_scalar_variables);
size_t i;
@ -869,7 +884,7 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
if (!get_keyval(conf, "lowerWalls", lower_walls, lower_walls) &&
b_null_lower_walls) {
cvm::log("Lower walls were not provided.\n");
lower_walls.resize(0);
lower_walls.clear();
}
bool b_null_upper_walls = false;
@ -884,7 +899,7 @@ int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
if (!get_keyval(conf, "upperWalls", upper_walls, upper_walls) &&
b_null_upper_walls) {
cvm::log("Upper walls were not provided.\n");
upper_walls.resize(0);
upper_walls.clear();
}
if ((lower_walls.size() == 0) && (upper_walls.size() == 0)) {
@ -954,7 +969,8 @@ void colvarbias_restraint_harmonic_walls::communicate_forces()
cvm::log("Communicating a force to colvar \""+
variables(i)->name+"\".\n");
}
variables(i)->add_bias_force_actual_value(colvar_forces[i]);
// Impulse-style multiple timestep
variables(i)->add_bias_force_actual_value(cvm::real(time_step_factor) * colvar_forces[i]);
}
}
@ -1282,9 +1298,9 @@ int colvarbias_restraint_histogram::init(std::string const &conf)
colvarbias_restraint_histogram::~colvarbias_restraint_histogram()
{
p.resize(0);
ref_p.resize(0);
p_diff.resize(0);
p.clear();
ref_p.clear();
p_diff.clear();
}
@ -1382,23 +1398,23 @@ std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
{
if (b_write_histogram) {
std::string file_name(cvm::output_prefix()+"."+this->name+".hist.dat");
std::ofstream os(file_name.c_str());
os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width)
<< " " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3)
<< ")\n";
std::ostream *os = cvm::proxy->output_stream(file_name);
*os << "# " << cvm::wrap_string(variables(0)->name, cvm::cv_width)
<< " " << "p(" << cvm::wrap_string(variables(0)->name, cvm::cv_width-3)
<< ")\n";
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+1)*width);
os << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< x_grid
<< " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< p[igrid] << "\n";
*os << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< x_grid
<< " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< p[igrid] << "\n";
}
os.close();
cvm::proxy->close_output_stream(file_name);
}
return os;
}