forked from lijiext/lammps
615 lines
19 KiB
C++
615 lines
19 KiB
C++
// -*- c++ -*-
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#include "colvarmodule.h"
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#include "colvarvalue.h"
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#include "colvarbias_restraint.h"
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colvarbias_restraint::colvarbias_restraint(char const *key)
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: colvarbias(key)
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{
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}
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int colvarbias_restraint::init(std::string const &conf)
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{
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colvarbias::init(conf);
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if (cvm::debug())
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cvm::log("Initializing a new restraint bias.\n");
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// TODO move these initializations to constructor and let get_keyval
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// only override existing values
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target_nstages = 0;
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target_nsteps = 0;
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force_k = 0.0;
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get_keyval(conf, "forceConstant", force_k, 1.0);
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{
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// get the initial restraint centers
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colvar_centers.resize(colvars.size());
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colvar_centers_raw.resize(colvars.size());
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size_t i;
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enable(f_cvb_apply_force);
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for (i = 0; i < colvars.size(); i++) {
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colvar_centers[i].type(colvars[i]->value());
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colvar_centers_raw[i].type(colvars[i]->value());
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if (cvm::debug()) {
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cvm::log("colvarbias_restraint: center size = "+
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cvm::to_str(colvar_centers[i].vector1d_value.size())+"\n");
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}
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}
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if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
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for (i = 0; i < colvars.size(); i++) {
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if (cvm::debug()) {
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cvm::log("colvarbias_restraint: parsing initial centers, i = "+cvm::to_str(i)+".\n");
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}
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colvar_centers[i].apply_constraints();
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colvar_centers_raw[i] = colvar_centers[i];
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}
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} else {
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colvar_centers.clear();
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cvm::error("Error: must define the initial centers of the restraints.\n");
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}
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if (colvar_centers.size() != colvars.size()) {
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cvm::error("Error: number of centers does not match "
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"that of collective variables.\n");
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}
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}
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{
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if (cvm::debug()) {
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cvm::log("colvarbias_restraint: parsing target centers.\n");
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}
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size_t i;
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if (get_keyval(conf, "targetCenters", target_centers, colvar_centers)) {
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if (colvar_centers.size() != colvars.size()) {
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cvm::error("Error: number of target centers does not match "
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"that of collective variables.\n");
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}
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b_chg_centers = true;
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for (i = 0; i < target_centers.size(); i++) {
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target_centers[i].apply_constraints();
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}
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} else {
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b_chg_centers = false;
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target_centers.clear();
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}
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}
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if (get_keyval(conf, "targetForceConstant", target_force_k, 0.0)) {
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if (b_chg_centers)
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cvm::error("Error: cannot specify both targetCenters and targetForceConstant.\n");
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starting_force_k = force_k;
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b_chg_force_k = true;
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get_keyval(conf, "targetEquilSteps", target_equil_steps, 0);
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get_keyval(conf, "lambdaSchedule", lambda_schedule, lambda_schedule);
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if (lambda_schedule.size()) {
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// There is one more lambda-point than stages
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target_nstages = lambda_schedule.size() - 1;
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}
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} else {
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b_chg_force_k = false;
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}
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if (b_chg_centers || b_chg_force_k) {
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get_keyval(conf, "targetNumSteps", target_nsteps, 0);
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if (!target_nsteps)
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cvm::error("Error: targetNumSteps must be non-zero.\n");
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if (get_keyval(conf, "targetNumStages", target_nstages, target_nstages) &&
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lambda_schedule.size()) {
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cvm::error("Error: targetNumStages and lambdaSchedule are incompatible.\n");
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}
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if (target_nstages) {
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// This means that either numStages of lambdaSchedule has been provided
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stage = 0;
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restraint_FE = 0.0;
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}
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if (get_keyval(conf, "targetForceExponent", force_k_exp, 1.0)) {
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if (! b_chg_force_k)
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cvm::log("Warning: not changing force constant: targetForceExponent will be ignored\n");
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if (force_k_exp < 1.0)
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cvm::log("Warning: for all practical purposes, targetForceExponent should be 1.0 or greater.\n");
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}
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}
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get_keyval(conf, "outputCenters", b_output_centers, false);
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if (b_chg_centers) {
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get_keyval(conf, "outputAccumulatedWork", b_output_acc_work, false);
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} else {
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b_output_acc_work = false;
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}
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acc_work = 0.0;
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if (cvm::debug())
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cvm::log("Done initializing a new restraint bias.\n");
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return COLVARS_OK;
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}
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colvarbias_restraint::~colvarbias_restraint()
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{
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if (cvm::n_rest_biases > 0)
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cvm::n_rest_biases -= 1;
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}
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void colvarbias_restraint::change_configuration(std::string const &conf)
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{
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get_keyval(conf, "forceConstant", force_k, force_k);
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if (get_keyval(conf, "centers", colvar_centers, colvar_centers)) {
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for (size_t i = 0; i < colvars.size(); i++) {
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colvar_centers[i].type(colvars[i]->value());
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colvar_centers[i].apply_constraints();
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colvar_centers_raw[i].type(colvars[i]->value());
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colvar_centers_raw[i] = colvar_centers[i];
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}
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}
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}
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cvm::real colvarbias_restraint::energy_difference(std::string const &conf)
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{
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std::vector<colvarvalue> alt_colvar_centers;
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cvm::real alt_force_k;
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cvm::real alt_bias_energy = 0.0;
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get_keyval(conf, "forceConstant", alt_force_k, force_k);
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alt_colvar_centers.resize(colvars.size());
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size_t i;
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for (i = 0; i < colvars.size(); i++) {
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alt_colvar_centers[i].type(colvars[i]->value());
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}
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if (get_keyval(conf, "centers", alt_colvar_centers, colvar_centers)) {
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for (i = 0; i < colvars.size(); i++) {
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alt_colvar_centers[i].apply_constraints();
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}
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}
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for (i = 0; i < colvars.size(); i++) {
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alt_bias_energy += restraint_potential(restraint_convert_k(alt_force_k, colvars[i]->width),
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colvars[i],
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alt_colvar_centers[i]);
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}
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return alt_bias_energy - bias_energy;
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}
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int colvarbias_restraint::update()
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{
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bias_energy = 0.0;
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if (cvm::debug())
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cvm::log("Updating the restraint bias \""+this->name+"\".\n");
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// Setup first stage of staged variable force constant calculation
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if (b_chg_force_k && target_nstages && cvm::step_absolute() == 0) {
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cvm::real lambda;
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if (lambda_schedule.size()) {
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lambda = lambda_schedule[0];
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} else {
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lambda = 0.0;
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}
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force_k = starting_force_k + (target_force_k - starting_force_k)
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* std::pow(lambda, force_k_exp);
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cvm::log("Restraint " + this->name + ", stage " +
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cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
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cvm::log("Setting force constant to " + cvm::to_str(force_k));
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}
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if (b_chg_centers) {
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if (!centers_incr.size()) {
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// if this is the first calculation, calculate the advancement
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// at each simulation step (or stage, if applicable)
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// (take current stage into account: it can be non-zero
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// if we are restarting a staged calculation)
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centers_incr.resize(colvars.size());
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for (size_t i = 0; i < colvars.size(); i++) {
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centers_incr[i].type(colvars[i]->value());
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centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) /
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cvm::real( target_nstages ? (target_nstages - stage) :
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(target_nsteps - cvm::step_absolute()));
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}
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if (cvm::debug()) {
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cvm::log("Center increment for the restraint bias \""+
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this->name+"\": "+cvm::to_str(centers_incr)+" at stage "+cvm::to_str(stage)+ ".\n");
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}
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}
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if (target_nstages) {
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if ((cvm::step_relative() > 0)
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&& (cvm::step_absolute() % target_nsteps) == 0
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&& stage < target_nstages) {
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for (size_t i = 0; i < colvars.size(); i++) {
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colvar_centers_raw[i] += centers_incr[i];
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colvar_centers[i] = colvar_centers_raw[i];
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colvars[i]->wrap(colvar_centers[i]);
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colvar_centers[i].apply_constraints();
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}
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stage++;
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cvm::log("Moving restraint \"" + this->name +
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"\" stage " + cvm::to_str(stage) +
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" : setting centers to " + cvm::to_str(colvar_centers) +
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" at step " + cvm::to_str(cvm::step_absolute()));
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}
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} else if ((cvm::step_relative() > 0) && (cvm::step_absolute() <= target_nsteps)) {
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// move the restraint centers in the direction of the targets
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// (slow growth)
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for (size_t i = 0; i < colvars.size(); i++) {
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colvar_centers_raw[i] += centers_incr[i];
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colvar_centers[i] = colvar_centers_raw[i];
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colvars[i]->wrap(colvar_centers[i]);
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colvar_centers[i].apply_constraints();
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}
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}
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if (cvm::debug())
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cvm::log("Current centers for the restraint bias \""+
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this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
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}
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if (b_chg_force_k) {
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// Coupling parameter, between 0 and 1
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cvm::real lambda;
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if (target_nstages) {
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// TI calculation: estimate free energy derivative
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// need current lambda
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if (lambda_schedule.size()) {
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lambda = lambda_schedule[stage];
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} else {
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lambda = cvm::real(stage) / cvm::real(target_nstages);
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}
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if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) {
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// Start averaging after equilibration period, if requested
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// Square distance normalized by square colvar width
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cvm::real dist_sq = 0.0;
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for (size_t i = 0; i < colvars.size(); i++) {
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dist_sq += colvars[i]->dist2(colvars[i]->value(), colvar_centers[i])
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/ (colvars[i]->width * colvars[i]->width);
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}
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restraint_FE += 0.5 * force_k_exp * std::pow(lambda, force_k_exp - 1.0)
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* (target_force_k - starting_force_k) * dist_sq;
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}
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// Finish current stage...
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if (cvm::step_absolute() % target_nsteps == 0 &&
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cvm::step_absolute() > 0) {
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cvm::log("Lambda= " + cvm::to_str(lambda) + " dA/dLambda= "
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+ cvm::to_str(restraint_FE / cvm::real(target_nsteps - target_equil_steps)));
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// ...and move on to the next one
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if (stage < target_nstages) {
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restraint_FE = 0.0;
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stage++;
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if (lambda_schedule.size()) {
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lambda = lambda_schedule[stage];
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} else {
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lambda = cvm::real(stage) / cvm::real(target_nstages);
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}
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force_k = starting_force_k + (target_force_k - starting_force_k)
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* std::pow(lambda, force_k_exp);
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cvm::log("Restraint " + this->name + ", stage " +
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cvm::to_str(stage) + " : lambda = " + cvm::to_str(lambda));
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cvm::log("Setting force constant to " + cvm::to_str(force_k));
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}
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}
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} else if (cvm::step_absolute() <= target_nsteps) {
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// update force constant (slow growth)
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lambda = cvm::real(cvm::step_absolute()) / cvm::real(target_nsteps);
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force_k = starting_force_k + (target_force_k - starting_force_k)
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* std::pow(lambda, force_k_exp);
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}
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}
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if (cvm::debug())
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cvm::log("Done updating the restraint bias \""+this->name+"\".\n");
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// Force and energy calculation
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for (size_t i = 0; i < colvars.size(); i++) {
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colvar_forces[i].type(colvars[i]->value());
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colvar_forces[i] = -1.0 * restraint_force(restraint_convert_k(force_k, colvars[i]->width),
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colvars[i],
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colvar_centers[i]);
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bias_energy += restraint_potential(restraint_convert_k(force_k, colvars[i]->width),
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colvars[i],
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colvar_centers[i]);
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if (cvm::debug()) {
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cvm::log("dist_grad["+cvm::to_str(i)+
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"] = "+cvm::to_str(colvars[i]->dist2_lgrad(colvars[i]->value(),
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colvar_centers[i]))+"\n");
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}
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}
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if (b_output_acc_work) {
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if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
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for (size_t i = 0; i < colvars.size(); i++) {
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// project forces on the calculated increments at this step
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acc_work += colvar_forces[i] * centers_incr[i];
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}
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}
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}
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if (cvm::debug())
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cvm::log("Current forces for the restraint bias \""+
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this->name+"\": "+cvm::to_str(colvar_forces)+".\n");
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return COLVARS_OK;
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}
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std::istream & colvarbias_restraint::read_restart(std::istream &is)
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{
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size_t const start_pos = is.tellg();
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cvm::log("Restarting restraint bias \""+
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this->name+"\".\n");
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std::string key, brace, conf;
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if ( !(is >> key) || !(key == "restraint" || key == "harmonic") ||
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!(is >> brace) || !(brace == "{") ||
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!(is >> colvarparse::read_block("configuration", conf)) ) {
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cvm::log("Error: in reading restart configuration for restraint bias \""+
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this->name+"\" at position "+
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cvm::to_str(is.tellg())+" in stream.\n");
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is.clear();
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is.seekg(start_pos, std::ios::beg);
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is.setstate(std::ios::failbit);
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return is;
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}
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// int id = -1;
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std::string name = "";
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// if ( ( (colvarparse::get_keyval (conf, "id", id, -1, colvarparse::parse_silent)) &&
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// (id != this->id) ) ||
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if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
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(name != this->name) )
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cvm::error("Error: in the restart file, the "
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"\"restraint\" block has a wrong name\n");
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// if ( (id == -1) && (name == "") ) {
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if (name.size() == 0) {
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cvm::error("Error: \"restraint\" block in the restart file "
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"has no identifiers.\n");
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}
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if (b_chg_centers) {
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// cvm::log ("Reading the updated restraint centers from the restart.\n");
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if (!get_keyval(conf, "centers", colvar_centers))
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cvm::error("Error: restraint centers are missing from the restart.\n");
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if (!get_keyval(conf, "centers_raw", colvar_centers_raw))
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cvm::error("Error: \"raw\" restraint centers are missing from the restart.\n");
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}
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if (b_chg_force_k) {
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// cvm::log ("Reading the updated force constant from the restart.\n");
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if (!get_keyval(conf, "forceConstant", force_k))
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cvm::error("Error: force constant is missing from the restart.\n");
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}
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if (target_nstages) {
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// cvm::log ("Reading current stage from the restart.\n");
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if (!get_keyval(conf, "stage", stage))
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cvm::error("Error: current stage is missing from the restart.\n");
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}
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if (b_output_acc_work) {
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if (!get_keyval(conf, "accumulatedWork", acc_work))
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cvm::error("Error: accumulatedWork is missing from the restart.\n");
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}
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is >> brace;
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if (brace != "}") {
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cvm::error("Error: corrupt restart information for restraint bias \""+
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this->name+"\": no matching brace at position "+
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cvm::to_str(is.tellg())+" in the restart file.\n");
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is.setstate(std::ios::failbit);
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}
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return is;
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}
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std::ostream & colvarbias_restraint::write_restart(std::ostream &os)
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{
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os << "restraint {\n"
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<< " configuration {\n"
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// << " id " << this->id << "\n"
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<< " name " << this->name << "\n";
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if (b_chg_centers) {
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size_t i;
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os << " centers ";
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for (i = 0; i < colvars.size(); i++) {
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os << " " << colvar_centers[i];
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}
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os << "\n";
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os << " centers_raw ";
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for (i = 0; i < colvars.size(); i++) {
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os << " " << colvar_centers_raw[i];
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}
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os << "\n";
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}
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if (b_chg_force_k) {
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os << " forceConstant "
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<< std::setprecision(cvm::en_prec)
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<< std::setw(cvm::en_width) << force_k << "\n";
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}
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if (target_nstages) {
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os << " stage " << std::setw(cvm::it_width)
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<< stage << "\n";
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}
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if (b_output_acc_work) {
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os << " accumulatedWork " << acc_work << "\n";
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}
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os << " }\n"
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<< "}\n\n";
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|
return os;
|
|
}
|
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|
|
|
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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(char const *key)
|
|
: colvarbias_restraint(key)
|
|
{
|
|
}
|
|
|
|
|
|
int colvarbias_restraint_harmonic::init(std::string const &conf)
|
|
{
|
|
colvarbias_restraint::init(conf);
|
|
|
|
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");
|
|
}
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
cvm::real colvarbias_restraint_harmonic::restraint_potential(cvm::real k,
|
|
colvar const *x,
|
|
colvarvalue const &xcenter) const
|
|
{
|
|
return 0.5 * k * x->dist2(x->value(), xcenter);
|
|
}
|
|
|
|
|
|
colvarvalue colvarbias_restraint_harmonic::restraint_force(cvm::real k,
|
|
colvar const *x,
|
|
colvarvalue const &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(char const *key)
|
|
: colvarbias_restraint(key)
|
|
{
|
|
}
|
|
|
|
|
|
int colvarbias_restraint_linear::init(std::string const &conf)
|
|
{
|
|
colvarbias_restraint::init(conf);
|
|
|
|
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");
|
|
}
|
|
return COLVARS_OK;
|
|
}
|
|
|
|
|
|
cvm::real colvarbias_restraint_linear::restraint_potential(cvm::real k,
|
|
colvar const *x,
|
|
colvarvalue const &xcenter) const
|
|
{
|
|
return k * (x->value() - xcenter);
|
|
}
|
|
|
|
|
|
colvarvalue colvarbias_restraint_linear::restraint_force(cvm::real k,
|
|
colvar const *x,
|
|
colvarvalue const &xcenter) const
|
|
{
|
|
return k;
|
|
}
|
|
|
|
|
|
cvm::real colvarbias_restraint_linear::restraint_convert_k(cvm::real k,
|
|
cvm::real dist_measure) const
|
|
{
|
|
return k / dist_measure;
|
|
}
|
|
|
|
|
|
|