colvarbias_restraint.cpp
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Created: Fri, Nov 8, 21:27

colvarbias_restraint.cpp
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	// -- c++ --

	#include "colvarmodule.h"
	#include "colvarvalue.h"
	#include "colvarbias_restraint.h"


	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());
	size_t i;

	enable(f_cvb_apply_force);

	for (i = 0; i < colvars.size(); i++) {
	colvar_centers[i].type(colvars[i]->value());
	colvar_centers_raw[i].type(colvars[i]->value());
	if (cvm::debug()) {
	cvm::log("colvarbias_restraint: center size = "+
	cvm::to_str(colvar_centers[i].vector1d_value.size())+"\n");
	}
	}
	if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
	for (i = 0; i < colvars.size(); i++) {
	if (cvm::debug()) {
	cvm::log("colvarbias_restraint: parsing initial centers, i = "+cvm::to_str(i)+".\n");
	}

	colvar_centers[i].apply_constraints();
	colvar_centers_raw[i] = colvar_centers[i];
	}
	} else {
	colvar_centers.clear();
	cvm::error("Error: must define the initial centers of the restraints.\n");
	}

	if (colvar_centers.size() != colvars.size()) {
	cvm::error("Error: number of centers does not match "
	"that of collective variables.\n");
	}
	}

	{
	if (cvm::debug()) {
	cvm::log("colvarbias_restraint: parsing target centers.\n");
	}

	size_t i;
	if (get_keyval(conf, "targetCenters", target_centers, colvar_centers)) {
	if (colvar_centers.size() != colvars.size()) {
	cvm::error("Error: number of target centers does not match "
	"that of collective variables.\n");
	}
	b_chg_centers = true;
	for (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::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::error("Error: targetNumSteps must be non-zero.\n");

	if (get_keyval(conf, "targetNumStages", target_nstages, target_nstages) &&
	lambda_schedule.size()) {
	cvm::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);
	if (b_chg_centers) {
	get_keyval(conf, "outputAccumulatedWork", b_output_acc_work, false);
	} else {
	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].type(colvars[i]->value());
	colvar_centers[i].apply_constraints();
	colvar_centers_raw[i].type(colvars[i]->value());
	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());
	size_t i;
	for (i = 0; i < colvars.size(); i++) {
	alt_colvar_centers[i].type(colvars[i]->value());
	}
	if (get_keyval(conf, "centers", alt_colvar_centers, colvar_centers)) {
	for (i = 0; i < colvars.size(); i++) {
	alt_colvar_centers[i].apply_constraints();
	}
	}

	for (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;
	}


	int 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]->value());
	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 \"" + this->name +
	"\" 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].type(colvars[i]->value());
	colvar_forces[i] = -1.0 * 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 (cvm::debug()) {
	cvm::log("dist_grad["+cvm::to_str(i)+
	"] = "+cvm::to_str(colvars[i]->dist2_lgrad(colvars[i]->value(),
	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 restraint bias \""+
	this->name+"\": "+cvm::to_str(colvar_forces)+".\n");

	return COLVARS_OK;
	}


	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::error("Error: in the restart file, the "
	"\"restraint\" block has a wrong name\n");
	// if ( (id == -1) && (name == "") ) {
	if (name.size() == 0) {
	cvm::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::error("Error: restraint centers are missing from the restart.\n");
	if (!get_keyval(conf, "centers_raw", colvar_centers_raw))
	cvm::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::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::error("Error: current stage is missing from the restart.\n");
	}

	if (b_output_acc_work) {
	if (!get_keyval(conf, "accumulatedWork", acc_work))
	cvm::error("Error: accumulatedWork is missing from the restart.\n");
	}

	is >> brace;
	if (brace != "}") {
	cvm::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) {
	size_t i;
	os << " centers ";
	for (i = 0; i < colvars.size(); i++) {
	os << " " << colvar_centers[i];
	}
	os << "\n";
	os << " centers_raw ";
	for (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;
	}

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