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colvarbias_restraint.cpp
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Fri, May 31, 14:17

colvarbias_restraint.cpp
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// -*- 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 "colvarmodule.h"
#include "colvarvalue.h"
#include "colvarbias_restraint.h"
colvarbias_restraint::colvarbias_restraint(char const *key)
: colvarbias(key)
{
}
int colvarbias_restraint::init(std::string const &conf)
{
colvarbias::init(conf);
enable(f_cvb_apply_force);
if (cvm::debug())
cvm::log("Initializing a new restraint bias.\n");
return COLVARS_OK;
}
int colvarbias_restraint::update()
{
// Update base class (bias_energy and colvar_forces are zeroed there)
colvarbias::update();
// Force and energy calculation
for (size_t i = 0; i < num_variables(); i++) {
bias_energy += restraint_potential(i);
colvar_forces[i].type(variables(i)->value());
colvar_forces[i].is_derivative();
colvar_forces[i] = restraint_force(i);
}
if (cvm::debug())
cvm::log("Done updating the restraint bias \""+this->name+"\".\n");
if (cvm::debug())
cvm::log("Current forces for the restraint bias \""+
this->name+"\": "+cvm::to_str(colvar_forces)+".\n");
return COLVARS_OK;
}
colvarbias_restraint::~colvarbias_restraint()
{
}
std::string const colvarbias_restraint::get_state_params() const
{
return colvarbias::get_state_params();
}
int colvarbias_restraint::set_state_params(std::string const &conf)
{
return colvarbias::set_state_params(conf);
}
std::ostream & colvarbias_restraint::write_traj_label(std::ostream &os)
{
return colvarbias::write_traj_label(os);
}
std::ostream & colvarbias_restraint::write_traj(std::ostream &os)
{
return colvarbias::write_traj(os);
}
colvarbias_restraint_centers::colvarbias_restraint_centers(char const *key)
: colvarbias(key), colvarbias_restraint(key)
{
}
int colvarbias_restraint_centers::init(std::string const &conf)
{
size_t i;
bool null_centers = (colvar_centers.size() == 0);
if (null_centers) {
// try to initialize the restraint centers for the first time
colvar_centers.resize(num_variables());
colvar_centers_raw.resize(num_variables());
for (i = 0; i < num_variables(); i++) {
colvar_centers[i].type(variables(i)->value());
colvar_centers[i].reset();
colvar_centers_raw[i].type(variables(i)->value());
colvar_centers_raw[i].reset();
}
}
if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
for (i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("colvarbias_restraint: parsing initial centers, i = "+cvm::to_str(i)+".\n");
}
colvar_centers_raw[i] = colvar_centers[i];
colvar_centers[i].apply_constraints();
}
null_centers = false;
}
if (null_centers) {
colvar_centers.clear();
cvm::error("Error: must define the initial centers of the restraints.\n", INPUT_ERROR);
return INPUT_ERROR;
}
if (colvar_centers.size() != num_variables()) {
cvm::error("Error: number of centers does not match "
"that of collective variables.\n", INPUT_ERROR);
return INPUT_ERROR;
}
return COLVARS_OK;
}
int colvarbias_restraint_centers::change_configuration(std::string const &conf)
{
if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < num_variables(); i++) {
colvar_centers[i].type(variables(i)->value());
colvar_centers[i].apply_constraints();
colvar_centers_raw[i].type(variables(i)->value());
colvar_centers_raw[i] = colvar_centers[i];
}
}
return COLVARS_OK;
}
colvarbias_restraint_k::colvarbias_restraint_k(char const *key)
: colvarbias(key), colvarbias_restraint(key)
{
force_k = -1.0;
}
int colvarbias_restraint_k::init(std::string const &conf)
{
get_keyval(conf, "forceConstant", force_k, (force_k > 0.0 ? force_k : 1.0));
if (force_k < 0.0) {
cvm::error("Error: undefined or invalid force constant.\n", INPUT_ERROR);
return INPUT_ERROR;
}
return COLVARS_OK;
}
int colvarbias_restraint_k::change_configuration(std::string const &conf)
{
get_keyval(conf, "forceConstant", force_k, force_k);
return COLVARS_OK;
}
colvarbias_restraint_moving::colvarbias_restraint_moving(char const *key)
{
target_nstages = 0;
target_nsteps = 0;
stage = 0;
b_chg_centers = false;
b_chg_force_k = false;
}
int colvarbias_restraint_moving::init(std::string const &conf)
{
if (b_chg_centers && b_chg_force_k) {
cvm::error("Error: cannot specify both targetCenters and targetForceConstant.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
if (b_chg_centers || b_chg_force_k) {
get_keyval(conf, "targetNumSteps", target_nsteps, target_nsteps);
if (!target_nsteps) {
cvm::error("Error: targetNumSteps must be non-zero.\n", INPUT_ERROR);
return cvm::get_error();
}
if (get_keyval(conf, "targetNumStages", target_nstages, target_nstages) &&
lambda_schedule.size()) {
cvm::error("Error: targetNumStages and lambdaSchedule are incompatible.\n", INPUT_ERROR);
return cvm::get_error();
}
}
return COLVARS_OK;
}
std::string const colvarbias_restraint_moving::get_state_params() const
{
std::ostringstream os;
os.setf(std::ios::scientific, std::ios::floatfield);
if (b_chg_centers || b_chg_force_k) {
// TODO move this
if (target_nstages) {
os << "stage " << std::setw(cvm::it_width)
<< stage << "\n";
}
}
return os.str();
}
int colvarbias_restraint_moving::set_state_params(std::string const &conf)
{
if (b_chg_centers || b_chg_force_k) {
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");
}
}
return COLVARS_OK;
}
colvarbias_restraint_centers_moving::colvarbias_restraint_centers_moving(char const *key)
: colvarbias(key),
colvarbias_restraint(key),
colvarbias_restraint_centers(key),
colvarbias_restraint_moving(key)
{
b_chg_centers = false;
b_output_centers = false;
b_output_acc_work = false;
acc_work = 0.0;
}
int colvarbias_restraint_centers_moving::init(std::string const &conf)
{
colvarbias_restraint_centers::init(conf);
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() != num_variables()) {
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();
}
}
if (b_chg_centers) {
// parse moving restraint options
colvarbias_restraint_moving::init(conf);
} else {
target_centers.clear();
return COLVARS_OK;
}
get_keyval(conf, "outputCenters", b_output_centers, b_output_centers);
get_keyval(conf, "outputAccumulatedWork", b_output_acc_work, b_output_acc_work);
return COLVARS_OK;
}
int colvarbias_restraint_centers_moving::update()
{
if (b_chg_centers) {
if (cvm::debug()) {
cvm::log("Updating centers for the restraint bias \""+
this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
}
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(num_variables());
for (size_t i = 0; i < num_variables(); i++) {
centers_incr[i].type(variables(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 < num_variables(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
variables(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 < num_variables(); i++) {
colvar_centers_raw[i] += centers_incr[i];
colvar_centers[i] = colvar_centers_raw[i];
variables(i)->wrap(colvar_centers[i]);
colvar_centers[i].apply_constraints();
}
}
if (cvm::debug()) {
cvm::log("New centers for the restraint bias \""+
this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
}
}
return COLVARS_OK;
}
int colvarbias_restraint_centers_moving::update_acc_work()
{
if (b_output_acc_work) {
if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
for (size_t i = 0; i < num_variables(); i++) {
// project forces on the calculated increments at this step
acc_work += colvar_forces[i] * centers_incr[i];
}
}
}
return COLVARS_OK;
}
std::string const colvarbias_restraint_centers_moving::get_state_params() const
{
std::ostringstream os;
os.setf(std::ios::scientific, std::ios::floatfield);
if (b_chg_centers) {
size_t i;
os << "centers ";
for (i = 0; i < num_variables(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< colvar_centers[i];
}
os << "\n";
os << "centers_raw ";
for (i = 0; i < num_variables(); i++) {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< colvar_centers_raw[i];
}
os << "\n";
if (b_output_acc_work) {
os << "accumulatedWork "
<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
<< acc_work << "\n";
}
}
return colvarbias_restraint_moving::get_state_params() + os.str();
}
int colvarbias_restraint_centers_moving::set_state_params(std::string const &conf)
{
colvarbias_restraint::set_state_params(conf);
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_output_acc_work) {
if (!get_keyval(conf, "accumulatedWork", acc_work))
cvm::error("Error: accumulatedWork is missing from the restart.\n");
}
}
return COLVARS_OK;
}
std::ostream & colvarbias_restraint_centers_moving::write_traj_label(std::ostream &os)
{
if (b_output_centers) {
for (size_t i = 0; i < num_variables(); i++) {
size_t const this_cv_width = (variables(i)->value()).output_width(cvm::cv_width);
os << " x0_"
<< cvm::wrap_string(variables(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_centers_moving::write_traj(std::ostream &os)
{
if (b_output_centers) {
for (size_t i = 0; i < num_variables(); 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_k_moving::colvarbias_restraint_k_moving(char const *key)
: colvarbias(key),
colvarbias_restraint(key),
colvarbias_restraint_k(key),
colvarbias_restraint_moving(key)
{
b_chg_force_k = false;
target_equil_steps = 0;
target_force_k = 0.0;
starting_force_k = 0.0;
force_k_exp = 1.0;
restraint_FE = 0.0;
}
int colvarbias_restraint_k_moving::init(std::string const &conf)
{
colvarbias_restraint_k::init(conf);
if (get_keyval(conf, "targetForceConstant", target_force_k, target_force_k)) {
starting_force_k = force_k;
b_chg_force_k = true;
}
if (b_chg_force_k) {
// parse moving restraint options
colvarbias_restraint_moving::init(conf);
} else {
return COLVARS_OK;
}
get_keyval(conf, "targetEquilSteps", target_equil_steps, target_equil_steps);
if (get_keyval(conf, "lambdaSchedule", lambda_schedule, lambda_schedule) &&
target_nstages > 0) {
cvm::error("Error: targetNumStages and lambdaSchedule are incompatible.\n", INPUT_ERROR);
return cvm::get_error();
}
if (lambda_schedule.size()) {
// There is one more lambda-point than stages
target_nstages = lambda_schedule.size() - 1;
}
if (get_keyval(conf, "targetForceExponent", force_k_exp, force_k_exp)) {
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");
}
return COLVARS_OK;
}
int colvarbias_restraint_k_moving::update()
{
if (b_chg_force_k) {
cvm::real lambda;
if (target_nstages) {
if (cvm::step_absolute() == 0) {
// Setup first stage of staged variable force constant calculation
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)
+ ", k = " + cvm::to_str(force_k));
}
// 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 < num_variables(); i++) {
dist_sq += d_restraint_potential_dk(i);
}
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("Restraint " + this->name + " 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)
+ ", k = " + 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);
}
}
return COLVARS_OK;
}
std::string const colvarbias_restraint_k_moving::get_state_params() const
{
std::ostringstream os;
os.setf(std::ios::scientific, std::ios::floatfield);
if (b_chg_force_k) {
os << "forceConstant "
<< std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << force_k << "\n";
}
return colvarbias_restraint_moving::get_state_params() + os.str();
}
int colvarbias_restraint_k_moving::set_state_params(std::string const &conf)
{
colvarbias_restraint::set_state_params(conf);
if (b_chg_force_k) {
// cvm::log ("Reading the updated force constant from the restart.\n");
if (!get_keyval(conf, "forceConstant", force_k, force_k))
cvm::error("Error: force constant is missing from the restart.\n");
}
return COLVARS_OK;
}
std::ostream & colvarbias_restraint_k_moving::write_traj_label(std::ostream &os)
{
return os;
}
std::ostream & colvarbias_restraint_k_moving::write_traj(std::ostream &os)
{
return os;
}
// redefined due to legacy state file keyword "harmonic"
std::istream & colvarbias_restraint::read_state(std::istream &is)
{
size_t const start_pos = is.tellg();
std::string key, brace, conf;
if ( !(is >> key) || !(key == "restraint" || key == "harmonic") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block("configuration", conf)) ||
(set_state_params(conf) != COLVARS_OK) ) {
cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR);
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
if (!read_state_data(is)) {
cvm::error("Error: in reading state data for \""+bias_type+"\" bias \""+
this->name+"\" at position "+
cvm::to_str(is.tellg())+" in stream.\n", INPUT_ERROR);
is.clear();
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
}
is >> brace;
if (brace != "}") {
cvm::log("brace = "+brace+"\n");
cvm::error("Error: corrupt restart information for \""+bias_type+"\" bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str(is.tellg())+" in stream.\n");
is.setstate(std::ios::failbit);
}
return is;
}
std::ostream & colvarbias_restraint::write_state(std::ostream &os)
{
os.setf(std::ios::scientific, std::ios::floatfield);
os << "restraint {\n"
<< " configuration {\n";
std::istringstream is(get_state_params());
std::string line;
while (std::getline(is, line)) {
os << " " << line << "\n";
}
os << " }\n";
write_state_data(os);
os << "}\n\n";
return os;
}
colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(char const *key)
: colvarbias(key),
colvarbias_restraint(key),
colvarbias_restraint_centers(key),
colvarbias_restraint_moving(key),
colvarbias_restraint_k(key),
colvarbias_restraint_centers_moving(key),
colvarbias_restraint_k_moving(key)
{
}
int colvarbias_restraint_harmonic::init(std::string const &conf)
{
colvarbias_restraint::init(conf);
colvarbias_restraint_moving::init(conf);
colvarbias_restraint_centers_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
for (size_t i = 0; i < num_variables(); i++) {
if (variables(i)->width != 1.0)
cvm::log("The force constant for colvar \""+variables(i)->name+
"\" will be rescaled to "+
cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+
" according to the specified width.\n");
}
return COLVARS_OK;
}
int colvarbias_restraint_harmonic::update()
{
// update parameters (centers or force constant)
colvarbias_restraint_centers_moving::update();
colvarbias_restraint_k_moving::update();
// update restraint energy and forces
colvarbias_restraint::update();
// update accumulated work using the current forces
colvarbias_restraint_centers_moving::update_acc_work();
return COLVARS_OK;
}
cvm::real colvarbias_restraint_harmonic::restraint_potential(size_t i) const
{
return 0.5 * force_k / (variables(i)->width * variables(i)->width) *
variables(i)->dist2(variables(i)->value(), colvar_centers[i]);
}
colvarvalue const colvarbias_restraint_harmonic::restraint_force(size_t i) const
{
return -0.5 * force_k / (variables(i)->width * variables(i)->width) *
variables(i)->dist2_lgrad(variables(i)->value(), colvar_centers[i]);
}
cvm::real colvarbias_restraint_harmonic::d_restraint_potential_dk(size_t i) const
{
return 0.5 / (variables(i)->width * variables(i)->width) *
variables(i)->dist2(variables(i)->value(), colvar_centers[i]);
}
std::string const colvarbias_restraint_harmonic::get_state_params() const
{
return colvarbias_restraint::get_state_params() +
colvarbias_restraint_centers_moving::get_state_params() +
colvarbias_restraint_k_moving::get_state_params();
}
int colvarbias_restraint_harmonic::set_state_params(std::string const &conf)
{
int error_code = COLVARS_OK;
error_code |= colvarbias_restraint::set_state_params(conf);
error_code |= colvarbias_restraint_centers_moving::set_state_params(conf);
error_code |= colvarbias_restraint_k_moving::set_state_params(conf);
return error_code;
}
std::ostream & colvarbias_restraint_harmonic::write_traj_label(std::ostream &os)
{
colvarbias_restraint::write_traj_label(os);
colvarbias_restraint_centers_moving::write_traj_label(os);
colvarbias_restraint_k_moving::write_traj_label(os);
return os;
}
std::ostream & colvarbias_restraint_harmonic::write_traj(std::ostream &os)
{
colvarbias_restraint::write_traj(os);
colvarbias_restraint_centers_moving::write_traj(os);
colvarbias_restraint_k_moving::write_traj(os);
return os;
}
int colvarbias_restraint_harmonic::change_configuration(std::string const &conf)
{
return colvarbias_restraint_centers::change_configuration(conf) |
colvarbias_restraint_k::change_configuration(conf);
}
cvm::real colvarbias_restraint_harmonic::energy_difference(std::string const &conf)
{
cvm::real const old_bias_energy = bias_energy;
cvm::real const old_force_k = force_k;
std::vector<colvarvalue> const old_centers = colvar_centers;
change_configuration(conf);
update();
cvm::real const result = (bias_energy - old_bias_energy);
bias_energy = old_bias_energy;
force_k = old_force_k;
colvar_centers = old_centers;
return result;
}
colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls(char const *key)
: colvarbias(key),
colvarbias_restraint(key),
colvarbias_restraint_k(key),
colvarbias_restraint_moving(key),
colvarbias_restraint_k_moving(key)
{
lower_wall_k = 0.0;
upper_wall_k = 0.0;
}
int colvarbias_restraint_harmonic_walls::init(std::string const &conf)
{
colvarbias_restraint::init(conf);
colvarbias_restraint_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
get_keyval(conf, "lowerWallConstant", lower_wall_k,
(lower_wall_k > 0.0) ? lower_wall_k : force_k);
get_keyval(conf, "upperWallConstant", upper_wall_k,
(upper_wall_k > 0.0) ? upper_wall_k : force_k);
enable(f_cvb_scalar_variables);
size_t i;
bool b_null_lower_walls = false;
if (lower_walls.size() == 0) {
b_null_lower_walls = true;
lower_walls.resize(num_variables());
for (i = 0; i < num_variables(); i++) {
lower_walls[i].type(variables(i)->value());
lower_walls[i].reset();
}
}
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);
}
bool b_null_upper_walls = false;
if (upper_walls.size() == 0) {
b_null_upper_walls = true;
upper_walls.resize(num_variables());
for (i = 0; i < num_variables(); i++) {
upper_walls[i].type(variables(i)->value());
upper_walls[i].reset();
}
}
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);
}
if ((lower_walls.size() == 0) && (upper_walls.size() == 0)) {
cvm::error("Error: no walls provided.\n", INPUT_ERROR);
return INPUT_ERROR;
}
if ((lower_walls.size() == 0) || (upper_walls.size() == 0)) {
for (i = 0; i < num_variables(); i++) {
if (variables(i)->is_enabled(f_cv_periodic)) {
cvm::error("Error: at least one variable is periodic, "
"both walls must be provided.\n", INPUT_ERROR);
return INPUT_ERROR;
}
}
}
if ((lower_walls.size() > 0) && (upper_walls.size() > 0)) {
for (i = 0; i < num_variables(); i++) {
if (lower_walls[i] >= upper_walls[i]) {
cvm::error("Error: one upper wall, "+
cvm::to_str(upper_walls[i])+
", is not higher than the lower wall, "+
cvm::to_str(lower_walls[i])+".\n",
INPUT_ERROR);
}
}
if (lower_wall_k * upper_wall_k == 0.0) {
cvm::error("Error: lowerWallConstant and upperWallConstant, "
"when defined, must both be positive.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
force_k = lower_wall_k * upper_wall_k;
// transform the two constants to relative values
// (allow changing both via force_k)
lower_wall_k /= force_k;
upper_wall_k /= force_k;
}
for (i = 0; i < num_variables(); i++) {
if (variables(i)->width != 1.0)
cvm::log("The force constant for colvar \""+variables(i)->name+
"\" will be rescaled to "+
cvm::to_str(force_k / (variables(i)->width * variables(i)->width))+
" according to the specified width.\n");
}
return COLVARS_OK;
}
int colvarbias_restraint_harmonic_walls::update()
{
colvarbias_restraint_k_moving::update();
colvarbias_restraint::update();
return COLVARS_OK;
}
void colvarbias_restraint_harmonic_walls::communicate_forces()
{
for (size_t i = 0; i < num_variables(); i++) {
if (cvm::debug()) {
cvm::log("Communicating a force to colvar \""+
variables(i)->name+"\".\n");
}
variables(i)->add_bias_force_actual_value(colvar_forces[i]);
}
}
cvm::real colvarbias_restraint_harmonic_walls::colvar_distance(size_t i) const
{
colvar *cv = variables(i);
colvarvalue const &cvv = variables(i)->actual_value();
// For a periodic colvar, both walls may be applicable at the same time
// in which case we pick the closer one
if (cv->is_enabled(f_cv_periodic)) {
cvm::real const lower_wall_dist2 = cv->dist2(cvv, lower_walls[i]);
cvm::real const upper_wall_dist2 = cv->dist2(cvv, upper_walls[i]);
if (lower_wall_dist2 < upper_wall_dist2) {
cvm::real const grad = cv->dist2_lgrad(cvv, lower_walls[i]);
if (grad < 0.0) { return 0.5 * grad; }
} else {
cvm::real const grad = cv->dist2_lgrad(cvv, upper_walls[i]);
if (grad > 0.0) { return 0.5 * grad; }
}
return 0.0;
}
if (lower_walls.size() > 0) {
cvm::real const grad = cv->dist2_lgrad(cvv, lower_walls[i]);
if (grad < 0.0) { return 0.5 * grad; }
}
if (upper_walls.size() > 0) {
cvm::real const grad = cv->dist2_lgrad(cvv, upper_walls[i]);
if (grad > 0.0) { return 0.5 * grad; }
}
return 0.0;
}
cvm::real colvarbias_restraint_harmonic_walls::restraint_potential(size_t i) const
{
cvm::real const dist = colvar_distance(i);
cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k;
return 0.5 * force_k * scale / (variables(i)->width * variables(i)->width) *
dist * dist;
}
colvarvalue const colvarbias_restraint_harmonic_walls::restraint_force(size_t i) const
{
cvm::real const dist = colvar_distance(i);
cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k;
return - force_k * scale / (variables(i)->width * variables(i)->width) * dist;
}
cvm::real colvarbias_restraint_harmonic_walls::d_restraint_potential_dk(size_t i) const
{
cvm::real const dist = colvar_distance(i);
cvm::real const scale = dist > 0.0 ? upper_wall_k : lower_wall_k;
return 0.5 * scale / (variables(i)->width * variables(i)->width) *
dist * dist;
}
std::string const colvarbias_restraint_harmonic_walls::get_state_params() const
{
return colvarbias_restraint::get_state_params() +
colvarbias_restraint_k_moving::get_state_params();
}
int colvarbias_restraint_harmonic_walls::set_state_params(std::string const &conf)
{
int error_code = COLVARS_OK;
error_code |= colvarbias_restraint::set_state_params(conf);
error_code |= colvarbias_restraint_k_moving::set_state_params(conf);
return error_code;
}
std::ostream & colvarbias_restraint_harmonic_walls::write_traj_label(std::ostream &os)
{
colvarbias_restraint::write_traj_label(os);
colvarbias_restraint_k_moving::write_traj_label(os);
return os;
}
std::ostream & colvarbias_restraint_harmonic_walls::write_traj(std::ostream &os)
{
colvarbias_restraint::write_traj(os);
colvarbias_restraint_k_moving::write_traj(os);
return os;
}
colvarbias_restraint_linear::colvarbias_restraint_linear(char const *key)
: colvarbias(key),
colvarbias_restraint(key),
colvarbias_restraint_centers(key),
colvarbias_restraint_moving(key),
colvarbias_restraint_k(key),
colvarbias_restraint_centers_moving(key),
colvarbias_restraint_k_moving(key)
{
}
int colvarbias_restraint_linear::init(std::string const &conf)
{
colvarbias_restraint::init(conf);
colvarbias_restraint_moving::init(conf);
colvarbias_restraint_centers_moving::init(conf);
colvarbias_restraint_k_moving::init(conf);
for (size_t i = 0; i < num_variables(); i++) {
if (variables(i)->is_enabled(f_cv_periodic)) {
cvm::error("Error: linear biases cannot be applied to periodic variables.\n",
INPUT_ERROR);
return INPUT_ERROR;
}
if (variables(i)->width != 1.0)
cvm::log("The force constant for colvar \""+variables(i)->name+
"\" will be rescaled to "+
cvm::to_str(force_k / variables(i)->width)+
" according to the specified width.\n");
}
return COLVARS_OK;
}
int colvarbias_restraint_linear::update()
{
// update parameters (centers or force constant)
colvarbias_restraint_centers_moving::update();
colvarbias_restraint_k_moving::update();
// update restraint energy and forces
colvarbias_restraint::update();
// update accumulated work using the current forces
colvarbias_restraint_centers_moving::update_acc_work();
return COLVARS_OK;
}
int colvarbias_restraint_linear::change_configuration(std::string const &conf)
{
// Only makes sense to change the force constant
return colvarbias_restraint_k::change_configuration(conf);
}
cvm::real colvarbias_restraint_linear::energy_difference(std::string const &conf)
{
cvm::real const old_bias_energy = bias_energy;
cvm::real const old_force_k = force_k;
change_configuration(conf);
update();
cvm::real const result = (bias_energy - old_bias_energy);
bias_energy = old_bias_energy;
force_k = old_force_k;
return result;
}
cvm::real colvarbias_restraint_linear::restraint_potential(size_t i) const
{
return force_k / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
}
colvarvalue const colvarbias_restraint_linear::restraint_force(size_t i) const
{
return -1.0 * force_k / variables(i)->width;
}
cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const
{
return 1.0 / variables(i)->width * (variables(i)->value() - colvar_centers[i]);
}
std::string const colvarbias_restraint_linear::get_state_params() const
{
return colvarbias_restraint::get_state_params() +
colvarbias_restraint_centers_moving::get_state_params() +
colvarbias_restraint_k_moving::get_state_params();
}
int colvarbias_restraint_linear::set_state_params(std::string const &conf)
{
int error_code = COLVARS_OK;
error_code |= colvarbias_restraint::set_state_params(conf);
error_code |= colvarbias_restraint_centers_moving::set_state_params(conf);
error_code |= colvarbias_restraint_k_moving::set_state_params(conf);
return error_code;
}
std::ostream & colvarbias_restraint_linear::write_traj_label(std::ostream &os)
{
colvarbias_restraint::write_traj_label(os);
colvarbias_restraint_centers_moving::write_traj_label(os);
colvarbias_restraint_k_moving::write_traj_label(os);
return os;
}
std::ostream & colvarbias_restraint_linear::write_traj(std::ostream &os)
{
colvarbias_restraint::write_traj(os);
colvarbias_restraint_centers_moving::write_traj(os);
colvarbias_restraint_k_moving::write_traj(os);
return os;
}
colvarbias_restraint_histogram::colvarbias_restraint_histogram(char const *key)
: colvarbias(key)
{
lower_boundary = 0.0;
upper_boundary = 0.0;
width = 0.0;
gaussian_width = 0.0;
}
int colvarbias_restraint_histogram::init(std::string const &conf)
{
colvarbias::init(conf);
get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary);
get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary);
get_keyval(conf, "width", width, width);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
}
get_keyval(conf, "gaussianWidth", gaussian_width, 2.0 * width, colvarparse::parse_silent);
get_keyval(conf, "gaussianSigma", gaussian_width, 2.0 * width);
if (lower_boundary >= upper_boundary) {
cvm::error("Error: the upper boundary, "+
cvm::to_str(upper_boundary)+
", is not higher than the lower boundary, "+
cvm::to_str(lower_boundary)+".\n",
INPUT_ERROR);
}
cvm::real const nbins = (upper_boundary - lower_boundary) / width;
int const nbins_round = (int)(nbins);
if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) {
cvm::log("Warning: grid interval ("+
cvm::to_str(lower_boundary, cvm::cv_width, cvm::cv_prec)+" - "+
cvm::to_str(upper_boundary, cvm::cv_width, cvm::cv_prec)+
") is not commensurate to its bin width ("+
cvm::to_str(width, cvm::cv_width, cvm::cv_prec)+").\n");
}
p.resize(nbins_round);
ref_p.resize(nbins_round);
p_diff.resize(nbins_round);
bool const inline_ref_p =
get_keyval(conf, "refHistogram", ref_p.data_array(), ref_p.data_array());
std::string ref_p_file;
get_keyval(conf, "refHistogramFile", ref_p_file, std::string(""));
if (ref_p_file.size()) {
if (inline_ref_p) {
cvm::error("Error: cannot specify both refHistogram and refHistogramFile at the same time.\n",
INPUT_ERROR);
} else {
std::ifstream is(ref_p_file.c_str());
std::string data_s = "";
std::string line;
while (getline_nocomments(is, line)) {
data_s.append(line+"\n");
}
if (data_s.size() == 0) {
cvm::error("Error: file \""+ref_p_file+"\" empty or unreadable.\n", FILE_ERROR);
}
is.close();
cvm::vector1d<cvm::real> data;
if (data.from_simple_string(data_s) != 0) {
cvm::error("Error: could not read histogram from file \""+ref_p_file+"\".\n");
}
if (data.size() == 2*ref_p.size()) {
// file contains both x and p(x)
size_t i;
for (i = 0; i < ref_p.size(); i++) {
ref_p[i] = data[2*i+1];
}
} else if (data.size() == ref_p.size()) {
ref_p = data;
} else {
cvm::error("Error: file \""+ref_p_file+"\" contains a histogram of different length.\n",
INPUT_ERROR);
}
}
}
cvm::real const ref_integral = ref_p.sum() * width;
if (std::fabs(ref_integral - 1.0) > 1.0e-03) {
cvm::log("Reference distribution not normalized, normalizing to unity.\n");
ref_p /= ref_integral;
}
get_keyval(conf, "writeHistogram", b_write_histogram, false);
get_keyval(conf, "forceConstant", force_k, 1.0);
return COLVARS_OK;
}
colvarbias_restraint_histogram::~colvarbias_restraint_histogram()
{
p.resize(0);
ref_p.resize(0);
p_diff.resize(0);
}
int colvarbias_restraint_histogram::update()
{
if (cvm::debug())
cvm::log("Updating the histogram restraint bias \""+this->name+"\".\n");
size_t vector_size = 0;
size_t icv;
for (icv = 0; icv < num_variables(); icv++) {
vector_size += variables(icv)->value().size();
}
cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size);
// calculate the histogram
p.reset();
for (icv = 0; icv < num_variables(); icv++) {
colvarvalue const &cv = variables(icv)->value();
if (cv.type() == colvarvalue::type_scalar) {
cvm::real const cv_value = cv.real_value;
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width));
}
} else if (cv.type() == colvarvalue::type_vector) {
size_t idim;
for (idim = 0; idim < cv.vector1d_value.size(); idim++) {
cvm::real const cv_value = cv.vector1d_value[idim];
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width));
}
}
} else {
cvm::error("Error: unsupported type for variable "+variables(icv)->name+".\n",
COLVARS_NOT_IMPLEMENTED);
return COLVARS_NOT_IMPLEMENTED;
}
}
cvm::real const force_k_cv = force_k * vector_size;
// calculate the difference between current and reference
p_diff = p - ref_p;
bias_energy = 0.5 * force_k_cv * p_diff * p_diff;
// calculate the forces
for (icv = 0; icv < num_variables(); icv++) {
colvarvalue const &cv = variables(icv)->value();
colvarvalue &cv_force = colvar_forces[icv];
cv_force.type(cv);
cv_force.reset();
if (cv.type() == colvarvalue::type_scalar) {
cvm::real const cv_value = cv.real_value;
cvm::real &force = cv_force.real_value;
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
force += force_k_cv * p_diff[igrid] *
norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width)) *
(-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
}
} else if (cv.type() == colvarvalue::type_vector) {
size_t idim;
for (idim = 0; idim < cv.vector1d_value.size(); idim++) {
cvm::real const cv_value = cv.vector1d_value[idim];
cvm::real &force = cv_force.vector1d_value[idim];
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
force += force_k_cv * p_diff[igrid] *
norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width)) *
(-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
}
}
} else {
// TODO
}
}
return COLVARS_OK;
}
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";
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.close();
}
return os;
}
std::istream & colvarbias_restraint_histogram::read_restart(std::istream &is)
{
return is;
}
std::ostream & colvarbias_restraint_histogram::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_restraint_histogram::write_traj(std::ostream &os)
{
os << " ";
if (b_output_energy) {
os << " "
<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
<< bias_energy;
}
return os;
}

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