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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12612 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-10-07 20:30:25 +00:00
parent 3c0612815f
commit 044084847b
33 changed files with 2284 additions and 2595 deletions
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566
lib/colvars/colvarbias.cpp
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@ -1,3 +1,5 @@
/// -*- c++ -*-
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarbias.h"
@ -27,12 +29,10 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
get_keyval (conf, "name", name, key_str+cvm::to_str (rank));
for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
bi != cvm::biases.end();
bi++) {
if ((*bi)->name == this->name)
cvm::fatal_error ("Error: this bias cannot have the same name, \""+this->name+
"\", as another bias.\n");
if (cvm::bias_by_name (this->name) != NULL) {
cvm::error ("Error: this bias cannot have the same name, \""+this->name+
"\", as another bias.\n", INPUT_ERROR);
return;
}
// lookup the associated colvars
@ -43,7 +43,8 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
}
}
if (!colvars.size()) {
cvm::fatal_error ("Error: no collective variables specified.\n");
cvm::error ("Error: no collective variables specified.\n");
return;
}
get_keyval (conf, "outputEnergy", b_output_energy, false);
@ -54,19 +55,45 @@ colvarbias::colvarbias()
: colvarparse(), has_data (false)
{}
colvarbias::~colvarbias()
{
// Remove references to this bias from colvars
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
++cvi) {
for (std::vector<colvarbias *>::iterator bi = (*cvi)->biases.begin();
bi != (*cvi)->biases.end();
++bi) {
if ( *bi == this) {
(*cvi)->biases.erase (bi);
break;
}
}
}
// ...and from the colvars module
for (std::vector<colvarbias *>::iterator bi = cvm::biases.begin();
bi != cvm::biases.end();
++bi) {
if ( *bi == this) {
cvm::biases.erase (bi);
break;
}
}
}
void colvarbias::add_colvar (std::string const &cv_name)
{
if (colvar *cvp = cvm::colvar_p (cv_name)) {
if (colvar *cvp = cvm::colvar_by_name (cv_name)) {
cvp->enable (colvar::task_gradients);
if (cvm::debug())
cvm::log ("Applying this bias to collective variable \""+
cvp->name+"\".\n");
colvars.push_back (cvp);
colvar_forces.push_back (colvarvalue (cvp->type()));
cvp->biases.push_back (this); // add back-reference to this bias to colvar
} else {
cvm::fatal_error ("Error: cannot find a colvar named \""+
cv_name+"\".\n");
cvm::error ("Error: cannot find a colvar named \""+
cv_name+"\".\n");
}
}
@ -86,13 +113,13 @@ void colvarbias::communicate_forces()
void colvarbias::change_configuration(std::string const &conf)
{
cvm::fatal_error ("Error: change_configuration() not implemented.\n");
cvm::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");
cvm::error ("Error: energy_difference() not implemented.\n");
return 0.;
}
@ -115,518 +142,3 @@ std::ostream & colvarbias::write_traj (std::ostream &os)
<< bias_energy;
return os;
}
colvarbias_restraint::colvarbias_restraint (std::string const &conf,
char const *key)
: colvarbias (conf, key),
target_nstages (0),
target_nsteps (0)
{
get_keyval (conf, "forceConstant", force_k, 1.0);
// get the initial restraint centers
colvar_centers.resize (colvars.size());
colvar_centers_raw.resize (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].type (colvars[i]->type());
colvar_centers_raw[i].type (colvars[i]->type());
}
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
colvar_centers_raw[i] = colvar_centers[i];
}
} else {
colvar_centers.clear();
cvm::fatal_error ("Error: must define the initial centers of the restraints.\n");
}
if (colvar_centers.size() != colvars.size())
cvm::fatal_error ("Error: number of centers does not match "
"that of collective variables.\n");
if (get_keyval (conf, "targetCenters", target_centers, colvar_centers)) {
b_chg_centers = true;
for (size_t i = 0; i < target_centers.size(); i++) {
target_centers[i].apply_constraints();
}
} else {
b_chg_centers = false;
target_centers.clear();
}
if (get_keyval (conf, "targetForceConstant", target_force_k, 0.0)) {
if (b_chg_centers)
cvm::fatal_error ("Error: cannot specify both targetCenters and targetForceConstant.\n");
starting_force_k = force_k;
b_chg_force_k = true;
get_keyval (conf, "targetEquilSteps", target_equil_steps, 0);
get_keyval (conf, "lambdaSchedule", lambda_schedule, lambda_schedule);
if (lambda_schedule.size()) {
// There is one more lambda-point than stages
target_nstages = lambda_schedule.size() - 1;
}
} else {
b_chg_force_k = false;
}
if (b_chg_centers || b_chg_force_k) {
get_keyval (conf, "targetNumSteps", target_nsteps, 0);
if (!target_nsteps)
cvm::fatal_error ("Error: targetNumSteps must be non-zero.\n");
if (get_keyval (conf, "targetNumStages", target_nstages, target_nstages) &&
lambda_schedule.size()) {
cvm::fatal_error ("Error: targetNumStages and lambdaSchedule are incompatible.\n");
}
if (target_nstages) {
// This means that either numStages of lambdaSchedule has been provided
stage = 0;
restraint_FE = 0.0;
}
if (get_keyval (conf, "targetForceExponent", force_k_exp, 1.0)) {
if (! b_chg_force_k)
cvm::log ("Warning: not changing force constant: targetForceExponent will be ignored\n");
if (force_k_exp < 1.0)
cvm::log ("Warning: for all practical purposes, targetForceExponent should be 1.0 or greater.\n");
}
}
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 restraint bias.\n");
}
colvarbias_restraint::~colvarbias_restraint ()
{
if (cvm::n_rest_biases > 0)
cvm::n_rest_biases -= 1;
}
void colvarbias_restraint::change_configuration (std::string const &conf)
{
get_keyval (conf, "forceConstant", force_k, force_k);
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
colvar_centers_raw[i] = colvar_centers[i];
}
}
}
cvm::real colvarbias_restraint::energy_difference (std::string const &conf)
{
std::vector<colvarvalue> alt_colvar_centers;
cvm::real alt_force_k;
cvm::real alt_bias_energy = 0.0;
get_keyval (conf, "forceConstant", alt_force_k, force_k);
alt_colvar_centers.resize (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
alt_colvar_centers[i].type (colvars[i]->type());
}
if (get_keyval (conf, "centers", alt_colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
}
}
for (size_t i = 0; i < colvars.size(); i++) {
alt_bias_energy += restraint_potential(restraint_convert_k(alt_force_k, colvars[i]->width),
colvars[i],
alt_colvar_centers[i]);
}
return alt_bias_energy - bias_energy;
}
cvm::real colvarbias_restraint::update()
{
bias_energy = 0.0;
if (cvm::debug())
cvm::log ("Updating the restraint bias \""+this->name+"\".\n");
// Setup first stage of staged variable force constant calculation
if (b_chg_force_k && target_nstages && cvm::step_absolute() == 0) {
cvm::real lambda;
if (lambda_schedule.size()) {
lambda = lambda_schedule[0];
} else {
lambda = 0.0;
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
cvm::log ("Restraint " + this->name + ", stage " +
cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
cvm::log ("Setting force constant to " + cvm::to_str (force_k));
}
if (b_chg_centers) {
if (!centers_incr.size()) {
// if this is the first calculation, calculate the advancement
// at each simulation step (or stage, if applicable)
// (take current stage into account: it can be non-zero
// if we are restarting a staged calculation)
centers_incr.resize (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
centers_incr[i].type (colvars[i]->type());
centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) /
cvm::real ( target_nstages ? (target_nstages - stage) :
(target_nsteps - cvm::step_absolute()));
}
if (cvm::debug())
cvm::log ("Center increment for the restraint bias \""+
this->name+"\": "+cvm::to_str (centers_incr)+" at stage "+cvm::to_str (stage)+ ".\n");
}
if (target_nstages) {
if ((cvm::step_relative() > 0)
&& (cvm::step_absolute() % target_nsteps) == 0
&& stage < target_nstages) {
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
colvars[i]->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
stage++;
cvm::log ("Moving restraint stage " + cvm::to_str(stage) +
" : setting centers to " + cvm::to_str (colvar_centers) +
" at step " + cvm::to_str (cvm::step_absolute()));
}
} else if ((cvm::step_relative() > 0) && (cvm::step_absolute() <= target_nsteps)) {
// move the restraint centers in the direction of the targets
// (slow growth)
for (size_t i = 0; i < colvars.size(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
colvars[i]->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
}
if (cvm::debug())
cvm::log ("Current centers for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_centers)+".\n");
}
if (b_chg_force_k) {
// Coupling parameter, between 0 and 1
cvm::real lambda;
if (target_nstages) {
// TI calculation: estimate free energy derivative
// need current lambda
if (lambda_schedule.size()) {
lambda = lambda_schedule[stage];
} else {
lambda = cvm::real(stage) / cvm::real(target_nstages);
}
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++) {
dist_sq += colvars[i]->dist2 (colvars[i]->value(), colvar_centers[i])
/ (colvars[i]->width * colvars[i]->width);
}
restraint_FE += 0.5 * force_k_exp * std::pow(lambda, force_k_exp - 1.0)
* (target_force_k - starting_force_k) * dist_sq;
}
// Finish current stage...
if (cvm::step_absolute() % target_nsteps == 0 &&
cvm::step_absolute() > 0) {
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) {
restraint_FE = 0.0;
stage++;
if (lambda_schedule.size()) {
lambda = lambda_schedule[stage];
} else {
lambda = cvm::real(stage) / cvm::real(target_nstages);
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
cvm::log ("Restraint " + this->name + ", stage " +
cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
cvm::log ("Setting force constant to " + cvm::to_str (force_k));
}
}
} else if (cvm::step_absolute() <= target_nsteps) {
// update force constant (slow growth)
lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps);
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
}
}
if (cvm::debug())
cvm::log ("Done updating the restraint bias \""+this->name+"\".\n");
// Force and energy calculation
for (size_t i = 0; i < colvars.size(); i++) {
colvar_forces[i] = -restraint_force(restraint_convert_k(force_k, colvars[i]->width),
colvars[i],
colvar_centers[i]);
bias_energy += restraint_potential(restraint_convert_k(force_k, colvars[i]->width),
colvars[i],
colvar_centers[i]);
}
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 restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
return bias_energy;
}
std::istream & colvarbias_restraint::read_restart (std::istream &is)
{
size_t const start_pos = is.tellg();
cvm::log ("Restarting restraint bias \""+
this->name+"\".\n");
std::string key, brace, conf;
if ( !(is >> key) || !(key == "restraint" || key == "harmonic") ||
!(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;
}
// int id = -1;
std::string name = "";
// if ( ( (colvarparse::get_keyval (conf, "id", id, -1, colvarparse::parse_silent)) &&
// (id != this->id) ) ||
if ( (colvarparse::get_keyval (conf, "name", name, std::string (""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::fatal_error ("Error: in the restart file, the "
"\"restraint\" block has a wrong name\n");
// if ( (id == -1) && (name == "") ) {
if (name.size() == 0) {
cvm::fatal_error ("Error: \"restraint\" block in the restart file "
"has no identifiers.\n");
}
if (b_chg_centers) {
// cvm::log ("Reading the updated restraint centers from the restart.\n");
if (!get_keyval (conf, "centers", colvar_centers))
cvm::fatal_error ("Error: restraint centers are missing from the restart.\n");
if (!get_keyval (conf, "centers_raw", colvar_centers_raw))
cvm::fatal_error ("Error: \"raw\" restraint centers are missing from the restart.\n");
}
if (b_chg_force_k) {
// cvm::log ("Reading the updated force constant from the restart.\n");
if (!get_keyval (conf, "forceConstant", force_k))
cvm::fatal_error ("Error: force constant is missing from the restart.\n");
}
if (target_nstages) {
// cvm::log ("Reading current stage from the restart.\n");
if (!get_keyval (conf, "stage", stage))
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 restraint 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;
}
std::ostream & colvarbias_restraint::write_restart (std::ostream &os)
{
os << "restraint {\n"
<< " configuration {\n"
// << " id " << this->id << "\n"
<< " name " << this->name << "\n";
if (b_chg_centers) {
os << " centers ";
for (size_t i = 0; i < colvars.size(); i++) {
os << " " << colvar_centers[i];
}
os << "\n";
os << " centers_raw ";
for (size_t i = 0; i < colvars.size(); i++) {
os << " " << colvar_centers_raw[i];
}
os << "\n";
}
if (b_chg_force_k) {
os << " forceConstant "
<< std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << force_k << "\n";
}
if (target_nstages) {
os << " stage " << std::setw (cvm::it_width)
<< stage << "\n";
}
if (b_output_acc_work) {
os << " accumulatedWork " << acc_work << "\n";
}
os << " }\n"
<< "}\n\n";
return os;
}
std::ostream & colvarbias_restraint::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_restraint::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;
}
colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(std::string const &conf, char const *key) :
colvarbias_restraint(conf, key) {
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->width != 1.0)
cvm::log ("The force constant for colvar \""+colvars[i]->name+
"\" will be rescaled to "+
cvm::to_str (restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
cvm::real colvarbias_restraint_harmonic::restraint_potential(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return 0.5 * k * x->dist2(x->value(), xcenter);
}
colvarvalue colvarbias_restraint_harmonic::restraint_force(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return 0.5 * k * x->dist2_lgrad(x->value(), xcenter);
}
cvm::real colvarbias_restraint_harmonic::restraint_convert_k(cvm::real k, cvm::real dist_measure) const
{
return k / (dist_measure * dist_measure);
}
colvarbias_restraint_linear::colvarbias_restraint_linear(std::string const &conf, char const *key) :
colvarbias_restraint(conf, key) {
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->width != 1.0)
cvm::log ("The force constant for colvar \""+colvars[i]->name+
"\" will be rescaled to "+
cvm::to_str (restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
cvm::real colvarbias_restraint_linear::restraint_potential(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return k * (x->value() - xcenter);
}
colvarvalue colvarbias_restraint_linear::restraint_force(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return k;
}
cvm::real colvarbias_restraint_linear::restraint_convert_k(cvm::real k, cvm::real dist_measure) const
{
return k / dist_measure;
}