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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12811 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-12-02 02:09:53 +00:00
parent 9c0f849594
commit c4af1cdbbd
34 changed files with 5927 additions and 4786 deletions
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265
lib/colvars/colvarbias_restraint.cpp
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@ -5,55 +5,74 @@
#include "colvarbias_restraint.h"
colvarbias_restraint::colvarbias_restraint (std::string const &conf,
char const *key)
: colvarbias (conf, key),
target_nstages (0),
target_nsteps (0)
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_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];
{
// get the initial restraint centers
colvar_centers.resize(colvars.size());
colvar_centers_raw.resize(colvars.size());
size_t i;
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");
}
}
} else {
colvar_centers.clear();
cvm::error ("Error: must define the initial centers of the restraints.\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");
}
if (colvar_centers.size() != colvars.size())
cvm::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();
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");
}
} else {
b_chg_centers = false;
target_centers.clear();
}
if (get_keyval (conf, "targetForceConstant", target_force_k, 0.0)) {
{
if (cvm::debug()) {
cvm::log("colvarbias_restraint: parsing target centers.\n");
}
size_t i;
if (get_keyval(conf, "targetCenters", target_centers, colvar_centers)) {
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");
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, "targetEquilSteps", target_equil_steps, 0);
get_keyval (conf, "lambdaSchedule", lambda_schedule, lambda_schedule);
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;
@ -63,13 +82,13 @@ colvarbias_restraint::colvarbias_restraint (std::string const &conf,
}
if (b_chg_centers || b_chg_force_k) {
get_keyval (conf, "targetNumSteps", target_nsteps, 0);
get_keyval(conf, "targetNumSteps", target_nsteps, 0);
if (!target_nsteps)
cvm::error ("Error: targetNumSteps must be non-zero.\n");
cvm::error("Error: targetNumSteps must be non-zero.\n");
if (get_keyval (conf, "targetNumStages", target_nstages, target_nstages) &&
if (get_keyval(conf, "targetNumStages", target_nstages, target_nstages) &&
lambda_schedule.size()) {
cvm::error ("Error: targetNumStages and lambdaSchedule are incompatible.\n");
cvm::error("Error: targetNumStages and lambdaSchedule are incompatible.\n");
}
if (target_nstages) {
@ -78,60 +97,63 @@ colvarbias_restraint::colvarbias_restraint (std::string const &conf,
restraint_FE = 0.0;
}
if (get_keyval (conf, "targetForceExponent", force_k_exp, 1.0)) {
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");
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");
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, "outputCenters", b_output_centers, false);
if (b_chg_centers) {
get_keyval (conf, "outputAccumulatedWork", b_output_acc_work, false);
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");
cvm::log("Done initializing a new restraint bias.\n");
}
colvarbias_restraint::~colvarbias_restraint ()
colvarbias_restraint::~colvarbias_restraint()
{
if (cvm::n_rest_biases > 0)
cvm::n_rest_biases -= 1;
}
void colvarbias_restraint::change_configuration (std::string const &conf)
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)) {
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)
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);
get_keyval(conf, "forceConstant", alt_force_k, force_k);
alt_colvar_centers.resize (colvars.size());
alt_colvar_centers.resize(colvars.size());
size_t i;
for (i = 0; i < colvars.size(); i++) {
alt_colvar_centers[i].type (colvars[i]->type());
alt_colvar_centers[i].type(colvars[i]->value());
}
if (get_keyval (conf, "centers", alt_colvar_centers, colvar_centers)) {
if (get_keyval(conf, "centers", alt_colvar_centers, colvar_centers)) {
for (i = 0; i < colvars.size(); i++) {
colvar_centers[i].type(colvars[i]->value());
colvar_centers[i].apply_constraints();
}
}
@ -151,7 +173,7 @@ cvm::real colvarbias_restraint::update()
bias_energy = 0.0;
if (cvm::debug())
cvm::log ("Updating the restraint bias \""+this->name+"\".\n");
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) {
@ -162,10 +184,10 @@ cvm::real colvarbias_restraint::update()
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 " +
* 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));
cvm::log("Setting force constant to " + cvm::to_str(force_k));
}
if (b_chg_centers) {
@ -175,16 +197,16 @@ cvm::real colvarbias_restraint::update()
// 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());
centers_incr.resize(colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
centers_incr[i].type (colvars[i]->type());
centers_incr[i].type(colvars[i]->value());
centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) /
cvm::real ( target_nstages ? (target_nstages - stage) :
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");
cvm::log("Center increment for the restraint bias \""+
this->name+"\": "+cvm::to_str(centers_incr)+" at stage "+cvm::to_str(stage)+ ".\n");
}
}
@ -200,10 +222,10 @@ cvm::real colvarbias_restraint::update()
colvar_centers[i].apply_constraints();
}
stage++;
cvm::log ("Moving restraint \"" + this->name +
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()));
" : 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
@ -217,8 +239,8 @@ cvm::real colvarbias_restraint::update()
}
if (cvm::debug())
cvm::log ("Current centers for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_centers)+".\n");
cvm::log("Current centers for the restraint bias \""+
this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
}
if (b_chg_force_k) {
@ -240,7 +262,7 @@ cvm::real colvarbias_restraint::update()
// 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])
dist_sq += colvars[i]->dist2(colvars[i]->value(), colvar_centers[i])
/ (colvars[i]->width * colvars[i]->width);
}
@ -252,8 +274,8 @@ cvm::real colvarbias_restraint::update()
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)));
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) {
@ -266,25 +288,26 @@ cvm::real colvarbias_restraint::update()
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 " +
* 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));
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);
* std::pow(lambda, force_k_exp);
}
}
if (cvm::debug())
cvm::log ("Done updating the restraint bias \""+this->name+"\".\n");
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]);
@ -292,8 +315,8 @@ cvm::real colvarbias_restraint::update()
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(),
cvm::log("dist_grad["+cvm::to_str(i)+
"] = "+cvm::to_str(colvars[i]->dist2_lgrad(colvars[i]->value(),
colvar_centers[i]))+"\n");
}
}
@ -308,31 +331,31 @@ cvm::real colvarbias_restraint::update()
}
if (cvm::debug())
cvm::log ("Current forces for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
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)
std::istream & colvarbias_restraint::read_restart(std::istream &is)
{
size_t const start_pos = is.tellg();
cvm::log ("Restarting restraint bias \""+
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)) ) {
!(is >> colvarparse::read_block("configuration", conf)) ) {
cvm::log ("Error: in reading restart configuration for restraint bias \""+
cvm::log("Error: in reading restart configuration for restraint bias \""+
this->name+"\" at position "+
cvm::to_str (is.tellg())+" in stream.\n");
cvm::to_str(is.tellg())+" in stream.\n");
is.clear();
is.seekg (start_pos, std::ios::beg);
is.setstate (std::ios::failbit);
is.seekg(start_pos, std::ios::beg);
is.setstate(std::ios::failbit);
return is;
}
@ -340,53 +363,53 @@ std::istream & colvarbias_restraint::read_restart (std::istream &is)
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)) &&
if ( (colvarparse::get_keyval(conf, "name", name, std::string(""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::error ("Error: in the restart file, the "
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 "
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 (!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 (!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 (!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");
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 \""+
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);
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)
std::ostream & colvarbias_restraint::write_restart(std::ostream &os)
{
os << "restraint {\n"
<< " configuration {\n"
@ -409,12 +432,12 @@ std::ostream & colvarbias_restraint::write_restart (std::ostream &os)
if (b_chg_force_k) {
os << " forceConstant "
<< std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << force_k << "\n";
<< std::setprecision(cvm::en_prec)
<< std::setw(cvm::en_width) << force_k << "\n";
}
if (target_nstages) {
os << " stage " << std::setw (cvm::it_width)
os << " stage " << std::setw(cvm::it_width)
<< stage << "\n";
}
@ -429,48 +452,48 @@ std::ostream & colvarbias_restraint::write_restart (std::ostream &os)
}
std::ostream & colvarbias_restraint::write_traj_label (std::ostream &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);
<< 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);
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);
<< 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);
<< cvm::wrap_string(this->name, cvm::en_width-2);
return os;
}
std::ostream & colvarbias_restraint::write_traj (std::ostream &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)
<< 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)
<< 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)
<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
<< acc_work;
return os;
@ -480,9 +503,9 @@ colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(std::string const &
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+
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))+
cvm::to_str(restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
@ -507,9 +530,9 @@ colvarbias_restraint_linear::colvarbias_restraint_linear(std::string const &conf
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+
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))+
cvm::to_str(restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}