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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-06-27 22:48:27 +00:00
parent 38112d0063
commit 4da20dce99
30 changed files with 883 additions and 571 deletions
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136
lib/colvars/colvarbias.cpp
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@ -41,10 +41,11 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
add_colvar (colvars_str[i]);
}
}
if (!colvars.size()) {
cvm::fatal_error ("Error: no collective variables specified.\n");
}
get_keyval (conf, "outputEnergy", b_output_energy, false);
}
@ -59,7 +60,7 @@ void colvarbias::add_colvar (std::string const &cv_name)
cvp->enable (colvar::task_gradients);
if (cvm::debug())
cvm::log ("Applying this bias to collective variable \""+
cvp->name+"\".\n");
cvp->name+"\".\n");
colvars.push_back (cvp);
colvar_forces.push_back (colvarvalue (cvp->type()));
} else {
@ -79,13 +80,47 @@ void colvarbias::communicate_forces()
}
colvars[i]->add_bias_force (colvar_forces[i]);
}
}
}
void colvarbias::change_configuration(std::string const &conf)
{
cvm::fatal_error ("Error: change_configuration() not implemented.\n");
}
cvm::real colvarbias::energy_difference(std::string const &conf)
{
cvm::fatal_error ("Error: energy_difference() not implemented.\n");
return 0.;
}
std::ostream & colvarbias::write_traj_label (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " E_"
<< cvm::wrap_string (this->name, cvm::en_width-2);
return os;
}
std::ostream & colvarbias::write_traj (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " "
<< bias_energy;
return os;
}
colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
char const *key)
: colvarbias (conf, key),
: colvarbias (conf, key),
target_nsteps (0),
target_nstages (0)
{
@ -171,25 +206,22 @@ colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
}
}
get_keyval (conf, "outputCenters", b_output_centers, false);
get_keyval (conf, "outputAccumulatedWork", b_output_acc_work, false);
acc_work = 0.0;
if (cvm::debug())
cvm::log ("Done initializing a new harmonic restraint bias.\n");
}
void colvarbias::change_configuration(std::string const &conf)
colvarbias_harmonic::~colvarbias_harmonic ()
{
cvm::fatal_error ("Error: change_configuration() not implemented.\n");
if (cvm::n_harm_biases > 0)
cvm::n_harm_biases -= 1;
}
cvm::real colvarbias::energy_difference(std::string const &conf)
{
cvm::fatal_error ("Error: energy_difference() not implemented.\n");
return 0.;
}
void colvarbias_harmonic::change_configuration(std::string const &conf)
void colvarbias_harmonic::change_configuration (std::string const &conf)
{
get_keyval (conf, "forceConstant", force_k, force_k);
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
@ -317,7 +349,7 @@ cvm::real colvarbias_harmonic::update()
if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) {
// Start averaging after equilibration period, if requested
// Square distance normalized by square colvar width
cvm::real dist_sq = 0.0;
for (size_t i = 0; i < colvars.size(); i++) {
@ -335,7 +367,7 @@ cvm::real colvarbias_harmonic::update()
cvm::log ("Lambda= " + cvm::to_str (lambda) + " dA/dLambda= "
+ cvm::to_str (restraint_FE / cvm::real(target_nsteps - target_equil_steps)));
// ...and move on to the next one
if (stage < target_nstages) {
@ -363,7 +395,7 @@ cvm::real colvarbias_harmonic::update()
if (cvm::debug())
cvm::log ("Done updating the harmonic bias \""+this->name+"\".\n");
// Force and energy calculation
for (size_t i = 0; i < colvars.size(); i++) {
colvar_forces[i] =
@ -379,6 +411,15 @@ cvm::real colvarbias_harmonic::update()
colvar_centers[i]))+"\n");
}
if (b_output_acc_work) {
if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
for (size_t i = 0; i < colvars.size(); i++) {
// project forces on the calculated increments at this step
acc_work += colvar_forces[i] * centers_incr[i];
}
}
}
if (cvm::debug())
cvm::log ("Current forces for the harmonic bias \""+
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
@ -408,7 +449,7 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
return is;
}
// int id = -1;
// int id = -1;
std::string name = "";
// if ( ( (colvarparse::get_keyval (conf, "id", id, -1, colvarparse::parse_silent)) &&
// (id != this->id) ) ||
@ -442,6 +483,11 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
cvm::fatal_error ("Error: current stage is missing from the restart.\n");
}
if (b_output_acc_work) {
if (!get_keyval (conf, "accumulatedWork", acc_work))
cvm::fatal_error ("Error: accumulatedWork is missing from the restart.\n");
}
is >> brace;
if (brace != "}") {
cvm::fatal_error ("Error: corrupt restart information for harmonic bias \""+
@ -484,9 +530,61 @@ std::ostream & colvarbias_harmonic::write_restart (std::ostream &os)
<< stage << "\n";
}
if (b_output_acc_work) {
os << " accumulatedWork " << acc_work << "\n";
}
os << " }\n"
<< "}\n\n";
return os;
}
std::ostream & colvarbias_harmonic::write_traj_label (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " E_"
<< cvm::wrap_string (this->name, cvm::en_width-2);
if (b_output_centers)
for (size_t i = 0; i < colvars.size(); i++) {
size_t const this_cv_width = (colvars[i]->value()).output_width (cvm::cv_width);
os << " x0_"
<< cvm::wrap_string (colvars[i]->name, this_cv_width-3);
}
if (b_output_acc_work)
os << " W_"
<< cvm::wrap_string (this->name, cvm::en_width-2);
return os;
}
std::ostream & colvarbias_harmonic::write_traj (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " "
<< std::setprecision (cvm::en_prec) << std::setw (cvm::en_width)
<< bias_energy;
if (b_output_centers)
for (size_t i = 0; i < colvars.size(); i++) {
os << " "
<< std::setprecision (cvm::cv_prec) << std::setw (cvm::cv_width)
<< colvar_centers[i];
}
if (b_output_acc_work)
os << " "
<< std::setprecision (cvm::en_prec) << std::setw (cvm::en_width)
<< acc_work;
return os;
}