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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12325 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-08-14 23:29:25 +00:00
parent 2fbbc61a1f
commit e3824e9332
6 changed files with 192 additions and 64 deletions
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7
lib/colvars/Makefile.g++
View File

@ -17,7 +17,7 @@ SHELL = /bin/sh
SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias.cpp colvarbias_meta.cpp \
colvar.cpp colvarcomp_angles.cpp colvarcomp.cpp colvarcomp_coordnums.cpp \
colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp \
colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp
colvargrid.cpp colvarmodule.cpp colvarparse.cpp colvarvalue.cpp colvarbias_alb.cpp
LIB = libcolvars.a
OBJ = $(SRC:.cpp=.o)
@ -60,6 +60,9 @@ colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarbias_abf.h \
colvarbias.h colvargrid.h
colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \
colvar.h colvarvalue.h colvarparse.h colvarbias_alb.h \
colvarbias.h
colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarbias.h colvar.h colvarparse.h
colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
@ -89,7 +92,7 @@ colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvargrid.h
colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvar.h colvarbias.h colvarbias_meta.h \
colvargrid.h colvarbias_abf.h
colvargrid.h colvarbias_abf.h colvarbias_alb.h
colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h
colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \

140
lib/colvars/colvarbias.cpp
View File

@ -14,8 +14,9 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
if (to_lower_cppstr (key_str) == std::string ("abf")) {
rank = cvm::n_abf_biases+1;
}
if (to_lower_cppstr (key_str) == std::string ("harmonic")) {
rank = cvm::n_harm_biases+1;
if (to_lower_cppstr (key_str) == std::string ("harmonic") ||
to_lower_cppstr (key_str) == std::string ("linear")) {
rank = cvm::n_rest_biases+1;
}
if (to_lower_cppstr (key_str) == std::string ("histogram")) {
rank = cvm::n_histo_biases+1;
@ -118,20 +119,13 @@ std::ostream & colvarbias::write_traj (std::ostream &os)
colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
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);
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 (force_k/(colvars[i]->width*colvars[i]->width))+
" according to the specified width.\n");
}
// get the initial restraint centers
colvar_centers.resize (colvars.size());
@ -151,7 +145,7 @@ colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
}
if (colvar_centers.size() != colvars.size())
cvm::fatal_error ("Error: number of harmonic centers does not match "
cvm::fatal_error ("Error: number of centers does not match "
"that of collective variables.\n");
if (get_keyval (conf, "targetCenters", target_centers, colvar_centers)) {
@ -211,17 +205,17 @@ colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
acc_work = 0.0;
if (cvm::debug())
cvm::log ("Done initializing a new harmonic restraint bias.\n");
cvm::log ("Done initializing a new restraint bias.\n");
}
colvarbias_harmonic::~colvarbias_harmonic ()
colvarbias_restraint::~colvarbias_restraint ()
{
if (cvm::n_harm_biases > 0)
cvm::n_harm_biases -= 1;
if (cvm::n_rest_biases > 0)
cvm::n_rest_biases -= 1;
}
void colvarbias_harmonic::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)) {
@ -233,7 +227,7 @@ void colvarbias_harmonic::change_configuration (std::string const &conf)
}
cvm::real colvarbias_harmonic::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;
@ -252,20 +246,21 @@ cvm::real colvarbias_harmonic::energy_difference (std::string const &conf)
}
for (size_t i = 0; i < colvars.size(); i++) {
alt_bias_energy += 0.5 * alt_force_k / (colvars[i]->width * colvars[i]->width) *
colvars[i]->dist2 (colvars[i]->value(), alt_colvar_centers[i]);
alt_bias_energy += restraint_potential(restraint_convert_k(alt_force_k, colvars[i]->width),
colvars[i],
alt_colvar_centers[i]);
}
return alt_bias_energy - bias_energy;
}
cvm::real colvarbias_harmonic::update()
cvm::real colvarbias_restraint::update()
{
bias_energy = 0.0;
if (cvm::debug())
cvm::log ("Updating the harmonic 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) {
@ -277,7 +272,7 @@ cvm::real colvarbias_harmonic::update()
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
cvm::log ("Harmonic restraint " + this->name + ", stage " +
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));
}
@ -297,7 +292,7 @@ cvm::real colvarbias_harmonic::update()
(target_nsteps - cvm::step_absolute()));
}
if (cvm::debug())
cvm::log ("Center increment for the harmonic bias \""+
cvm::log ("Center increment for the restraint bias \""+
this->name+"\": "+cvm::to_str (centers_incr)+" at stage "+cvm::to_str (stage)+ ".\n");
}
@ -330,7 +325,7 @@ cvm::real colvarbias_harmonic::update()
}
if (cvm::debug())
cvm::log ("Current centers for the harmonic bias \""+
cvm::log ("Current centers for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_centers)+".\n");
}
@ -380,7 +375,7 @@ cvm::real colvarbias_harmonic::update()
}
force_k = starting_force_k + (target_force_k - starting_force_k)
* std::pow (lambda, force_k_exp);
cvm::log ("Harmonic restraint " + this->name + ", stage " +
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));
}
@ -394,21 +389,16 @@ cvm::real colvarbias_harmonic::update()
}
if (cvm::debug())
cvm::log ("Done updating the harmonic 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] =
(-0.5) * force_k /
(colvars[i]->width * colvars[i]->width) *
colvars[i]->dist2_lgrad (colvars[i]->value(),
colvar_centers[i]);
bias_energy += 0.5 * force_k / (colvars[i]->width * colvars[i]->width) *
colvars[i]->dist2(colvars[i]->value(), colvar_centers[i]);
if (cvm::debug())
cvm::log ("dist_grad["+cvm::to_str (i)+
"] = "+cvm::to_str (colvars[i]->dist2_lgrad (colvars[i]->value(),
colvar_centers[i]))+"\n");
colvar_forces[i] = -restraint_force(restraint_convert_k(force_k, colvars[i]->width),
colvars[i],
colvar_centers[i]);
bias_energy += restraint_potential(restraint_convert_k(force_k, colvars[i]->width),
colvars[i],
colvar_centers[i]);
}
if (b_output_acc_work) {
@ -421,26 +411,26 @@ cvm::real colvarbias_harmonic::update()
}
if (cvm::debug())
cvm::log ("Current forces for the harmonic bias \""+
cvm::log ("Current forces for the restraint bias \""+
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
return bias_energy;
}
std::istream & colvarbias_harmonic::read_restart (std::istream &is)
std::istream & colvarbias_restraint::read_restart (std::istream &is)
{
size_t const start_pos = is.tellg();
cvm::log ("Restarting harmonic bias \""+
cvm::log ("Restarting restraint bias \""+
this->name+"\".\n");
std::string key, brace, conf;
if ( !(is >> key) || !(key == "harmonic") ||
if ( !(is >> key) || !(key == "restraint" || key == "harmonic") ||
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block ("configuration", conf)) ) {
cvm::log ("Error: in reading restart configuration for harmonic bias \""+
cvm::log ("Error: in reading restart configuration for restraint bias \""+
this->name+"\" at position "+
cvm::to_str (is.tellg())+" in stream.\n");
is.clear();
@ -456,10 +446,10 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
if ( (colvarparse::get_keyval (conf, "name", name, std::string (""), colvarparse::parse_silent)) &&
(name != this->name) )
cvm::fatal_error ("Error: in the restart file, the "
"\"harmonic\" block has a wrong name\n");
"\"restraint\" block has a wrong name\n");
// if ( (id == -1) && (name == "") ) {
if (name.size() == 0) {
cvm::fatal_error ("Error: \"harmonic\" block in the restart file "
cvm::fatal_error ("Error: \"restraint\" block in the restart file "
"has no identifiers.\n");
}
@ -490,7 +480,7 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
is >> brace;
if (brace != "}") {
cvm::fatal_error ("Error: corrupt restart information for harmonic bias \""+
cvm::fatal_error ("Error: corrupt restart information for restraint bias \""+
this->name+"\": no matching brace at position "+
cvm::to_str (is.tellg())+" in the restart file.\n");
is.setstate (std::ios::failbit);
@ -499,9 +489,9 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
}
std::ostream & colvarbias_harmonic::write_restart (std::ostream &os)
std::ostream & colvarbias_restraint::write_restart (std::ostream &os)
{
os << "harmonic {\n"
os << "restraint {\n"
<< " configuration {\n"
// << " id " << this->id << "\n"
<< " name " << this->name << "\n";
@ -541,7 +531,7 @@ std::ostream & colvarbias_harmonic::write_restart (std::ostream &os)
}
std::ostream & colvarbias_harmonic::write_traj_label (std::ostream &os)
std::ostream & colvarbias_restraint::write_traj_label (std::ostream &os)
{
os << " ";
@ -564,7 +554,7 @@ std::ostream & colvarbias_harmonic::write_traj_label (std::ostream &os)
}
std::ostream & colvarbias_harmonic::write_traj (std::ostream &os)
std::ostream & colvarbias_restraint::write_traj (std::ostream &os)
{
os << " ";
@ -588,3 +578,55 @@ std::ostream & colvarbias_harmonic::write_traj (std::ostream &os)
return os;
}
colvarbias_restraint_harmonic::colvarbias_restraint_harmonic(std::string const &conf, char const *key) :
colvarbias_restraint(conf, key) {
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->width != 1.0)
cvm::log ("The force constant for colvar \""+colvars[i]->name+
"\" will be rescaled to "+
cvm::to_str (restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
cvm::real colvarbias_restraint_harmonic::restraint_potential(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return 0.5 * k * x->dist2(x->value(), xcenter);
}
colvarvalue colvarbias_restraint_harmonic::restraint_force(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return 0.5 * k * x->dist2_lgrad(x->value(), xcenter);
}
cvm::real colvarbias_restraint_harmonic::restraint_convert_k(cvm::real k, cvm::real dist_measure) const
{
return k / (dist_measure * dist_measure);
}
colvarbias_restraint_linear::colvarbias_restraint_linear(std::string const &conf, char const *key) :
colvarbias_restraint(conf, key) {
for (size_t i = 0; i < colvars.size(); i++) {
if (colvars[i]->width != 1.0)
cvm::log ("The force constant for colvar \""+colvars[i]->name+
"\" will be rescaled to "+
cvm::to_str (restraint_convert_k(force_k, colvars[i]->width))+
" according to the specified width.\n");
}
}
cvm::real colvarbias_restraint_linear::restraint_potential(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return k * (x->value() - xcenter);
}
colvarvalue colvarbias_restraint_linear::restraint_force(cvm::real k, colvar* x, const colvarvalue &xcenter) const
{
return k;
}
cvm::real colvarbias_restraint_linear::restraint_convert_k(cvm::real k, cvm::real dist_measure) const
{
return k / dist_measure;
}

54
lib/colvars/colvarbias.h
View File

@ -82,9 +82,9 @@ protected:
};
/// \brief Harmonic restraint, optionally moving towards a target
/// \brief Bias restraint, optionally moving towards a target
/// (implementation of \link colvarbias \endlink)
class colvarbias_harmonic : public colvarbias {
class colvarbias_restraint : public colvarbias {
public:
@ -110,14 +110,23 @@ public:
virtual std::ostream & write_traj (std::ostream &os);
/// \brief Constructor
colvarbias_harmonic (std::string const &conf, char const *key);
colvarbias_restraint (std::string const &conf, char const *key);
/// Destructor
virtual ~colvarbias_harmonic();
virtual ~colvarbias_restraint();
protected:
/// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const = 0;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const = 0;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const = 0;
/// \brief Restraint centers
std::vector<colvarvalue> colvar_centers;
@ -143,7 +152,6 @@ protected:
/// \brief Accumulated work
cvm::real acc_work;
/// \brief Restraint force constant
cvm::real force_k;
@ -182,6 +190,42 @@ protected:
size_t target_nsteps;
};
/// \brief Harmonic bias restraint
/// (implementation of \link colvarbias_restraint \endlink)
class colvarbias_restraint_harmonic : public colvarbias_restraint {
public:
colvarbias_restraint_harmonic(std::string const &conf, char const *key);
protected: /// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
/// \brief Linear bias restraint
/// (implementation of \link colvarbias_restraint \endlink)
class colvarbias_restraint_linear : public colvarbias_restraint {
public:
colvarbias_restraint_linear(std::string const &conf, char const *key);
protected: /// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
#endif

2
lib/colvars/colvarcomp.h
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@ -601,7 +601,7 @@ protected:
std::vector<cvm::atom_pos> ref_pos;
/// Geometric center of the reference coordinates
cvm::atom_pos ref_pos_center;
cvm::atom_pos ref_pos_center;
/// Eigenvector (of a normal or essential mode): will always have zero center
std::vector<cvm::rvector> eigenvec;

47
lib/colvars/colvarmodule.cpp
View File

@ -4,6 +4,7 @@
#include "colvarproxy.h"
#include "colvar.h"
#include "colvarbias.h"
#include "colvarbias_alb.h"
#include "colvarbias_meta.h"
#include "colvarbias_abf.h"
@ -247,10 +248,10 @@ void colvarmodule::init_biases (std::string const &conf)
if (harm_conf.size()) {
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_harmonic (harm_conf, "harmonic"));
biases.push_back (new colvarbias_restraint_harmonic (harm_conf, "harmonic"));
(biases.back())->check_keywords (harm_conf, "harmonic");
cvm::decrease_depth();
n_harm_biases++;
n_rest_biases++;
} else {
cvm::log ("Warning: \"harmonic\" keyword found without configuration.\n");
}
@ -258,6 +259,45 @@ void colvarmodule::init_biases (std::string const &conf)
}
}
{
/// initialize linear restraints
std::string lin_conf = "";
size_t lin_pos = 0;
while (parse->key_lookup (conf, "linear", lin_conf, lin_pos)) {
if (lin_conf.size()) {
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_restraint_linear (lin_conf, "linear"));
(biases.back())->check_keywords (lin_conf, "linear");
cvm::decrease_depth();
n_rest_biases++;
} else {
cvm::log ("Warning: \"linear\" keyword found without configuration.\n");
}
lin_conf = "";
}
}
{
/// initialize adaptive linear biases
std::string alb_conf = "";
size_t alb_pos = 0;
while (parse->key_lookup (conf, "ALB", alb_conf, alb_pos)) {
if (alb_conf.size()) {
cvm::log (cvm::line_marker);
cvm::increase_depth();
biases.push_back (new colvarbias_alb (alb_conf, "ALB"));
(biases.back())->check_keywords (alb_conf, "ALB");
cvm::decrease_depth();
n_rest_biases++;
} else {
cvm::log ("Warning: \"ALB\" keyword found without configuration.\n");
}
alb_conf = "";
}
}
{
/// initialize histograms
std::string histo_conf = "";
@ -815,7 +855,6 @@ void cvm::read_index_file (char const *filename)
}
void cvm::load_atoms (char const *file_name,
std::vector<cvm::atom> &atoms,
std::string const &pdb_field,
@ -893,7 +932,7 @@ void cvm::load_coords_xyz (char const *filename,
std::vector<colvar *> colvarmodule::colvars;
std::vector<colvarbias *> colvarmodule::biases;
size_t colvarmodule::n_abf_biases = 0;
size_t colvarmodule::n_harm_biases = 0;
size_t colvarmodule::n_rest_biases = 0;
size_t colvarmodule::n_histo_biases = 0;
size_t colvarmodule::n_meta_biases = 0;
colvarproxy *colvarmodule::proxy = NULL;

6
lib/colvars/colvarmodule.h
View File

@ -2,7 +2,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2014-05-08"
#define COLVARS_VERSION "2014-08-13"
#endif
#ifndef COLVARS_DEBUG
@ -142,9 +142,9 @@ public:
/// \brief Number of metadynamics biases initialized (in normal
/// conditions should be 1)
static size_t n_meta_biases;
/// \brief Number of harmonic biases initialized (no limit on the
/// \brief Number of restraint biases initialized (no limit on the
/// number)
static size_t n_harm_biases;
static size_t n_rest_biases;
/// \brief Number of histograms initialized (no limit on the
/// number)
static size_t n_histo_biases;