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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10118 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-06-27 22:48:27 +00:00
parent 38112d0063
commit 4da20dce99
30 changed files with 883 additions and 571 deletions
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14
lib/colvars/Makefile.g++
View File

@ -1,4 +1,4 @@
# library build makefile for colvars module
# library build -*- makefile -*- for colvars module
# which file will be copied to Makefile.lammps
@ -14,9 +14,9 @@ SHELL = /bin/sh
# ------ DEFINITIONS ------
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 \
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
LIB = libcolvars.a
@ -25,11 +25,13 @@ EXE = #colvars_standalone
# ------ MAKE PROCEDURE ------
default: $(LIB) $(EXE)
default: $(LIB) $(EXE) Makefile.lammps
Makefile.lammps:
@cp $(EXTRAMAKE) Makefile.lammps
$(LIB): $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
$(CXX) -o $@ $(CXXFLAGS) $^

70
lib/colvars/Makefile.mingw32-cross
View File

@ -1,4 +1,4 @@
# library build makefile for colvars module
# library build -*- makefile -*- for colvars module
# which file will be copied to Makefile.lammps
@ -6,35 +6,42 @@ EXTRAMAKE = Makefile.lammps.empty
# ------ SETTINGS ------
CXX = i686-pc-mingw32-g++
CXX = i686-w64-mingw32-g++
CXXFLAGS = -O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64 \
-fno-rtti -fno-exceptions -finline-functions \
-ffast-math -funroll-loops -fstrict-aliasing \
-Wall -W -Wno-uninitialized
ARCHIVE = i686-pc-mingw32-ar
ARCHIVE = i686-w64-mingw32-ar
ARCHFLAG = -rscv
SHELL = /bin/sh
# ------ DEFINITIONS ------
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 \
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
LIB = libcolvars.a
OBJ = $(SRC:.cpp=.o)
DIR = Obj_mingw32/
LIB = $(DIR)libcolvars.a
OBJ = $(SRC:%.cpp=$(DIR)%.o)
EXE = #colvars_standalone
# ------ MAKE PROCEDURE ------
default: $(LIB) $(EXE)
default: $(DIR) $(LIB) $(EXE) Makefile.lammps
$(LIB): $(OBJ)
$(DIR):
mkdir $(DIR)
Makefile.lammps:
@cp $(EXTRAMAKE) Makefile.lammps
$(LIB): $(DIR) $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
@cp $(EXTRAMAKE) Makefile.lammps
colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
$(DIR)colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
$(CXX) -o $@ $(CXXFLAGS) $^
# ------ MAKE FLAGS ------
@ -46,58 +53,59 @@ colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)
# ------ COMPILE RULES ------
.cpp.o:
$(CXX) $(CXXFLAGS) -c $<
$(DIR)%.o: %.cpp
$(CXX) $(CXXFLAGS) -c $< -o $@
# ------ DEPENDENCIES ------
#
colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvars_main.o: colvars_main.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarproxy_standalone.h colvaratoms.h colvarparse.h colvarvalue.h
colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
$(DIR)colvarproxy_standalone.o: colvarproxy_standalone.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvaratoms.h colvarparse.h colvarvalue.h \
colvarproxy_standalone.h
colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarparse.h colvarvalue.h colvaratoms.h
colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \
$(DIR)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.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)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 \
$(DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h \
colvarbias_meta.h colvarbias.h colvargrid.h
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h
colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
$(DIR)colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvar.h colvarvalue.h colvarparse.h colvarcomp.h \
colvaratoms.h
colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvar.h colvarparse.h colvarcomp.h colvaratoms.h
colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
$(DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarparse.h colvarvalue.h colvaratoms.h \
colvar.h colvarcomp.h
colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
$(DIR)colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
$(DIR)colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \
colvarproxy.h colvarvalue.h colvarparse.h colvar.h colvarcomp.h \
colvaratoms.h
colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
$(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \
colvarcomp.h colvaratoms.h
colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvar.h colvarcomp.h colvaratoms.h \
colvargrid.h
colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)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
colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h
colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
$(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h
# ------ CLEAN ------
clean:
-rm *.o *~ $(LIB)
-rm $(DIR)*.o *~ $(LIB)
-rmdir $(DIR)

17
lib/colvars/README
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@ -4,9 +4,24 @@ that allows enhanced sampling in molecular dynamics simulations.
The module is written to maximize performance, portability,
flexibility of usage for the user, and extensibility for the developer.
The following publication describes the principles of
The development of the colvars library is now hosted on github at:
http://colvars.github.io/
You can use this site to get access to the latest development sources
and the up-to-date documentation.
Copy of the specific documentation is also in
doc/PDF/colvars-refman-lammps.pdf
Please report bugs and request new features at:
https://github.com/colvars/colvars/issues
The following publications describe the principles of
the implementation of this library:
Using collective variables to drive molecular dynamics simulations,
Giacomo Fiorin , Michael L. Klein & Jérôme Hénin (2013):
Molecular Physics DOI:10.1080/00268976.2013.813594
Exploring Multidimensional Free Energy Landscapes Using
Time-Dependent Biases on Collective Variables,
J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein,

81
lib/colvars/colvar.cpp
View File

@ -14,7 +14,7 @@
colvar::colvar (std::string const &conf)
{
cvm::log ("Initializing a new collective variable.\n");
get_keyval (conf, "name", this->name,
(std::string ("colvar")+cvm::to_str (cvm::colvars.size()+1)));
@ -26,7 +26,7 @@ colvar::colvar (std::string const &conf)
"\", as another colvar.\n");
}
// all tasks disabled by default
// all tasks disabled by default
for (size_t i = 0; i < task_ntot; i++) {
tasks[i] = false;
}
@ -152,7 +152,7 @@ colvar::colvar (std::string const &conf)
// Decide whether the colvar is periodic
// Used to wrap extended DOF if extendedLagrangian is on
if (cvcs.size() == 1 && (cvcs[0])->b_periodic && (cvcs[0])->sup_np == 1
if (cvcs.size() == 1 && (cvcs[0])->b_periodic && (cvcs[0])->sup_np == 1
&& (cvcs[0])->sup_coeff == 1.0 ) {
this->b_periodic = true;
this->period = (cvcs[0])->period;
@ -167,6 +167,9 @@ colvar::colvar (std::string const &conf)
// check the available features of each cvc
for (size_t i = 0; i < cvcs.size(); i++) {
if ((cvcs[i])->b_debug_gradients)
enable (task_gradients);
if ((cvcs[i])->sup_np != 1) {
if (cvm::debug() && b_linear)
cvm::log ("Warning: You are using a non-linear polynomial "
@ -307,7 +310,7 @@ colvar::colvar (std::string const &conf)
cvm::log ("Enabling the extended Lagrangian term for colvar \""+
this->name+"\".\n");
enable (task_extended_lagrangian);
xr.type (this->type());
@ -525,10 +528,10 @@ void colvar::enable (colvar::task const &t)
if ( !tasks[task_extended_lagrangian] ) {
enable (task_gradients);
if (!b_Jacobian_force)
if (!b_Jacobian_force)
cvm::fatal_error ("Error: colvar \""+this->name+
"\" does not have Jacobian forces implemented.\n");
if (!b_linear)
if (!b_linear)
cvm::fatal_error ("Error: colvar \""+this->name+
"\" must be defined as a linear combination "
"to calculate the Jacobian force.\n");
@ -664,12 +667,24 @@ void colvar::disable (colvar::task const &t)
}
void colvar::setup() {
// loop over all components to reset masses of all groups
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
atoms.read_positions();
atoms.reset_mass(name,i,ig);
}
}
}
colvar::~colvar()
{
for (size_t i = 0; i < cvcs.size(); i++) {
delete cvcs[i];
}
}
}
@ -682,6 +697,8 @@ void colvar::calc()
cvm::log ("Calculating colvar \""+this->name+"\".\n");
// prepare atom groups for calculation
if (cvm::debug())
cvm::log ("Collecting data from atom groups.\n");
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
@ -697,19 +714,21 @@ void colvar::calc()
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_velocities();
}
}
}
}
if (tasks[task_system_force]) {
for (size_t i = 0; i < cvcs.size(); i++) {
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvcs[i]->atom_groups[ig]->read_system_forces();
}
}
}
}
// calculate the value of the colvar
if (cvm::debug())
cvm::log ("Calculating colvar components.\n");
x.reset();
if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
@ -727,7 +746,7 @@ void colvar::calc()
( ((cvcs[i])->sup_np != 1) ?
std::pow ((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
(cvcs[i])->value().real_value );
}
}
} else {
// only linear combination allowed
@ -741,7 +760,7 @@ void colvar::calc()
cvm::to_str ((cvcs[i])->value(),
cvm::cv_width, cvm::cv_prec)+".\n");
x += (cvcs[i])->sup_coeff * (cvcs[i])->value();
}
}
}
if (cvm::debug())
@ -762,9 +781,9 @@ void colvar::calc()
// if requested, propagate (via chain rule) the gradients above
// to the atoms used to define the roto-translation
for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
cvcs[i]->atom_groups[ig]->calc_fit_gradients();
}
}
cvm::decrease_depth();
}
@ -801,7 +820,7 @@ void colvar::calc()
for (size_t k = 0; k < cvcs[i]->atom_groups[j]->size(); k++) {
int a = std::lower_bound (atom_ids.begin(), atom_ids.end(),
cvcs[i]->atom_groups[j]->at(k).id) - atom_ids.begin();
atomic_gradients[a] += coeff * cvcs[i]->atom_groups[j]->at(k).grad;
atomic_gradients[a] += coeff * cvcs[i]->atom_groups[j]->at(k).grad;
}
}
}
@ -925,7 +944,7 @@ cvm::real colvar::update()
}
if (tasks[task_Jacobian_force]) {
cvm::increase_depth();
for (size_t i = 0; i < cvcs.size(); i++) {
(cvcs[i])->calc_Jacobian_derivative();
@ -941,8 +960,8 @@ cvm::real colvar::update()
fj *= cvm::boltzmann() * cvm::temperature();
// the instantaneous Jacobian force was not included in the reported system force;
// instead, it is subtracted from the applied force (silent Jacobian correction)
if (! tasks[task_report_Jacobian_force])
// instead, it is subtracted from the applied force (silent Jacobian correction)
if (! tasks[task_report_Jacobian_force])
f -= fj;
}
@ -966,9 +985,9 @@ cvm::real colvar::update()
// leap to v_(i+1/2)
if (tasks[task_langevin]) {
vr -= dt * ext_gamma * vr.real_value;
vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
}
vr += (0.5 * dt) * fr / ext_mass;
vr += dt * ext_sigma * cvm::rand_gaussian() / ext_mass;
}
vr += (0.5 * dt) * fr / ext_mass;
xr += dt * vr;
xr.apply_constraints();
if (this->b_periodic) this->wrap (xr);
@ -989,13 +1008,13 @@ cvm::real colvar::update()
void colvar::communicate_forces()
{
if (cvm::debug())
cvm::log ("Communicating forces from colvar \""+this->name+"\".\n");
cvm::log ("Communicating forces from colvar \""+this->name+"\".\n");
if (x.type() == colvarvalue::type_scalar) {
for (size_t i = 0; i < cvcs.size(); i++) {
cvm::increase_depth();
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff *
(cvcs[i])->apply_force (f * (cvcs[i])->sup_coeff *
cvm::real ((cvcs[i])->sup_np) *
(std::pow ((cvcs[i])->value().real_value,
(cvcs[i])->sup_np-1)) );
@ -1012,7 +1031,7 @@ void colvar::communicate_forces()
}
if (cvm::debug())
cvm::log ("Done communicating forces from colvar \""+this->name+"\".\n");
cvm::log ("Done communicating forces from colvar \""+this->name+"\".\n");
}
@ -1200,7 +1219,7 @@ std::istream & colvar::read_traj (std::istream &is)
is >> ft;
if (tasks[task_extended_lagrangian]) {
if (tasks[task_extended_lagrangian]) {
is >> fr;
ft_reported = fr;
} else {
@ -1248,7 +1267,7 @@ std::ostream & colvar::write_restart (std::ostream &os) {
os << "}\n\n";
return os;
}
}
std::ostream & colvar::write_traj_label (std::ostream & os)
@ -1418,7 +1437,7 @@ inline void history_add_value (size_t const &history_length,
inline void history_incr (std::list< std::list<colvarvalue> > &history,
std::list< std::list<colvarvalue> >::iterator &history_p)
{
if ((++history_p) == history.end())
if ((++history_p) == history.end())
history_p = history.begin();
}
@ -1435,7 +1454,7 @@ void colvar::calc_acf()
// first-step operations
colvar *cfcv = (acf_colvar_name.size() ?
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_p (acf_colvar_name) :
this);
if (cfcv->type() != this->type())
@ -1474,7 +1493,7 @@ void colvar::calc_acf()
} else {
colvar *cfcv = (acf_colvar_name.size() ?
colvar *cfcv = (acf_colvar_name.size() ?
cvm::colvar_p (acf_colvar_name) :
this);
@ -1539,7 +1558,7 @@ void colvar::calc_vel_acf (std::list<colvarvalue> &v_list,
// inner products of previous velocities with current (acf_i and
// vs_i are updated)
colvarvalue::inner_opt (v, vs_i, v_list.end(), acf_i);
colvarvalue::inner_opt (v, vs_i, v_list.end(), acf_i);
acf_nframes++;
}
@ -1559,7 +1578,7 @@ void colvar::calc_coor_acf (std::list<colvarvalue> &x_list,
*(acf_i++) += x.norm2();
colvarvalue::inner_opt (x, xs_i, x_list.end(), acf_i);
colvarvalue::inner_opt (x, xs_i, x_list.end(), acf_i);
acf_nframes++;
}
@ -1581,7 +1600,7 @@ void colvar::calc_p2coor_acf (std::list<colvarvalue> &x_list,
// value of P2(0) = 1
*(acf_i++) += 1.0;
colvarvalue::p2leg_opt (x, xs_i, x_list.end(), acf_i);
colvarvalue::p2leg_opt (x, xs_i, x_list.end(), acf_i);
acf_nframes++;
}

7
lib/colvars/colvar.h
View File

@ -215,7 +215,7 @@ protected:
cvm::real ext_gamma;
/// Amplitude of Gaussian white noise for Langevin extended dynamics
cvm::real ext_sigma;
/// \brief Harmonic restraint force
colvarvalue fr;
@ -288,6 +288,9 @@ public:
/// Disable the specified task
void disable (colvar::task const &t);
/// Get ready for a run and possibly re-initialize internal data
void setup();
/// Destructor
~colvar();
@ -380,7 +383,7 @@ protected:
colvarvalue x_old;
/// Time series of values and velocities used in correlation
/// functions
/// functions
std::list< std::list<colvarvalue> > acf_x_history, acf_v_history;
/// Time series of values and velocities used in correlation
/// functions (pointers)x

57
lib/colvars/colvaratoms.cpp
View File

@ -26,8 +26,8 @@ cvm::atom_group::atom_group (std::string const &conf,
cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
noforce (false)
{
this->reserve (atoms.size());
@ -43,8 +43,8 @@ cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
cvm::atom_group::atom_group()
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
: b_dummy (false), b_center (false), b_rotate (false),
ref_pos_group (NULL), b_fit_gradients (false),
noforce (false)
{
total_mass = 0.0;
@ -71,6 +71,18 @@ void cvm::atom_group::add_atom (cvm::atom const &a)
}
void cvm::atom_group::reset_mass(std::string &name, int i, int j)
{
total_mass = 0.0;
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
total_mass += ai->mass;
}
cvm::log ("Re-initialized atom group "+name+":"+cvm::to_str (i)+"/"+
cvm::to_str (j)+". "+ cvm::to_str (this->size())+
" atoms: total mass = "+cvm::to_str (this->total_mass)+".\n");
}
void cvm::atom_group::parse (std::string const &conf,
char const *key)
{
@ -129,6 +141,25 @@ void cvm::atom_group::parse (std::string const &conf,
atom_indexes.clear();
}
std::string index_group_name;
if (get_keyval (group_conf, "indexGroup", index_group_name)) {
// use an index group from the index file read globally
std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
std::list<std::vector<int> >::iterator index_groups_i = cvm::index_groups.begin();
for ( ; names_i != cvm::index_group_names.end() ; names_i++, index_groups_i++) {
if (*names_i == index_group_name)
break;
}
if (names_i == cvm::index_group_names.end()) {
cvm::fatal_error ("Error: could not find index group "+
index_group_name+" among those provided by the index file.\n");
}
this->reserve (index_groups_i->size());
for (size_t i = 0; i < index_groups_i->size(); i++) {
this->push_back (cvm::atom ((*index_groups_i)[i]));
}
}
}
{
@ -234,7 +265,7 @@ void cvm::atom_group::parse (std::string const &conf,
}
}
for (std::vector<cvm::atom>::iterator a1 = this->begin();
for (std::vector<cvm::atom>::iterator a1 = this->begin();
a1 != this->end(); a1++) {
std::vector<cvm::atom>::iterator a2 = a1;
++a2;
@ -253,10 +284,10 @@ void cvm::atom_group::parse (std::string const &conf,
if (get_keyval (group_conf, "dummyAtom", dummy_atom_pos, cvm::atom_pos(), mode)) {
b_dummy = true;
this->total_mass = 1.0;
} else
} else
b_dummy = false;
if (b_dummy && (this->size()))
if (b_dummy && (this->size()))
cvm::fatal_error ("Error: cannot set up group \""+
std::string (key)+"\" as a dummy atom "
"and provide it with atom definitions.\n");
@ -328,7 +359,7 @@ void cvm::atom_group::parse (std::string const &conf,
std::string ref_pos_col;
double ref_pos_col_value;
if (get_keyval (group_conf, "refPositionsCol", ref_pos_col, std::string (""), mode)) {
// if provided, use PDB column to select coordinates
bool found = get_keyval (group_conf, "refPositionsColValue", ref_pos_col_value, 0.0, mode);
@ -486,7 +517,7 @@ void cvm::atom_group::calc_apply_roto_translation()
}
}
void cvm::atom_group::apply_translation (cvm::rvector const &t)
void cvm::atom_group::apply_translation (cvm::rvector const &t)
{
if (b_dummy) return;
@ -496,7 +527,7 @@ void cvm::atom_group::apply_translation (cvm::rvector const &t)
}
}
void cvm::atom_group::apply_rotation (cvm::rotation const &rot)
void cvm::atom_group::apply_rotation (cvm::rotation const &rot)
{
if (b_dummy) return;
@ -617,11 +648,11 @@ void cvm::atom_group::calc_fit_gradients()
}
if (b_rotate) {
// add the rotation matrix contribution to the gradients
cvm::rotation const rot_inv = rot.inverse();
cvm::atom_pos const cog = this->center_of_geometry();
for (size_t i = 0; i < this->size(); i++) {
cvm::atom_pos const pos_orig = rot_inv.rotate ((b_center ? ((*this)[i].pos - cog) : ((*this)[i].pos)));
@ -785,7 +816,7 @@ void cvm::atom_group::apply_force (cvm::rvector const &force)
for (cvm::atom_iter ai = this->begin();
ai != this->end(); ai++) {
ai->apply_force ((ai->mass/this->total_mass) * force);
}
}
}
}

25
lib/colvars/colvaratoms.h
View File

@ -8,7 +8,7 @@
/// \brief Stores numeric id, mass and all mutable data for an atom,
/// mostly used by a \link cvc \endlink
///
///
/// This class may be used (although not necessarily) to keep atomic
/// data (id, mass, position and collective variable derivatives)
/// altogether. There may be multiple instances with identical
@ -23,7 +23,7 @@ protected:
/// \brief Index in the list of atoms involved by the colvars (\b
/// NOT in the global topology!)
size_t index;
int index;
public:
@ -47,7 +47,7 @@ public:
/// \brief Gradient of a scalar collective variable with respect
/// to this atom
///
///
/// This can only handle a scalar collective variable (i.e. when
/// the \link colvarvalue::real_value \endlink member is used
/// from the \link colvarvalue \endlink class), which is also the
@ -57,8 +57,8 @@ public:
/// implementation
cvm::rvector grad;
/// \brief Default constructor, setting id to a non-valid value
inline atom() {}
/// \brief Default constructor, setting id and index to invalid numbers
atom() : id (-1), index (-1) { reset_data(); }
/// \brief Initialize an atom for collective variable calculation
/// and get its internal identifier \param atom_number Atom index in
@ -121,7 +121,7 @@ class colvarmodule::atom_group
public colvarparse
{
public:
// Note: all members here are kept public, to make possible to any
// Note: all members here are kept public, to allow any
// object accessing and manipulating them
@ -138,7 +138,7 @@ public:
/// Allocates and populates the sorted list of atom ids
void create_sorted_ids (void);
/// \brief When updating atomic coordinates, translate them to align with the
/// center of mass of the reference coordinates
@ -175,7 +175,7 @@ public:
/// \brief If b_center or b_rotate is true, use this group to
/// define the transformation (default: this group itself)
atom_group *ref_pos_group;
/// Total mass of the atom group
cvm::real total_mass;
@ -199,9 +199,14 @@ public:
/// \brief Initialize the group after a temporary vector of atoms
atom_group (std::vector<cvm::atom> const &atoms);
/// \brief Add an atom to this group
/// \brief Add an atom to this group
void add_atom (cvm::atom const &a);
/// \brief Re-initialize the total mass of a group.
/// This is needed in case the hosting MD code has an option to
/// change atom masses after their initialization.
void reset_mass (std::string &name, int i, int j);
/// \brief Default constructor
atom_group();
@ -216,7 +221,7 @@ public:
void calc_apply_roto_translation();
/// \brief Save center of geometry fo ref positions,
/// then subtract it
/// then subtract it
void center_ref_pos();
/// \brief Move all positions

136
lib/colvars/colvarbias.cpp
View File

@ -41,10 +41,11 @@ colvarbias::colvarbias (std::string const &conf, char const *key)
add_colvar (colvars_str[i]);
}
}
if (!colvars.size()) {
cvm::fatal_error ("Error: no collective variables specified.\n");
}
get_keyval (conf, "outputEnergy", b_output_energy, false);
}
@ -59,7 +60,7 @@ void colvarbias::add_colvar (std::string const &cv_name)
cvp->enable (colvar::task_gradients);
if (cvm::debug())
cvm::log ("Applying this bias to collective variable \""+
cvp->name+"\".\n");
cvp->name+"\".\n");
colvars.push_back (cvp);
colvar_forces.push_back (colvarvalue (cvp->type()));
} else {
@ -79,13 +80,47 @@ void colvarbias::communicate_forces()
}
colvars[i]->add_bias_force (colvar_forces[i]);
}
}
}
void colvarbias::change_configuration(std::string const &conf)
{
cvm::fatal_error ("Error: change_configuration() not implemented.\n");
}
cvm::real colvarbias::energy_difference(std::string const &conf)
{
cvm::fatal_error ("Error: energy_difference() not implemented.\n");
return 0.;
}
std::ostream & colvarbias::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::write_traj (std::ostream &os)
{
os << " ";
if (b_output_energy)
os << " "
<< bias_energy;
return os;
}
colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
char const *key)
: colvarbias (conf, key),
: colvarbias (conf, key),
target_nsteps (0),
target_nstages (0)
{
@ -171,25 +206,22 @@ colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
}
}
get_keyval (conf, "outputCenters", b_output_centers, false);
get_keyval (conf, "outputAccumulatedWork", b_output_acc_work, false);
acc_work = 0.0;
if (cvm::debug())
cvm::log ("Done initializing a new harmonic restraint bias.\n");
}
void colvarbias::change_configuration(std::string const &conf)
colvarbias_harmonic::~colvarbias_harmonic ()
{
cvm::fatal_error ("Error: change_configuration() not implemented.\n");
if (cvm::n_harm_biases > 0)
cvm::n_harm_biases -= 1;
}
cvm::real colvarbias::energy_difference(std::string const &conf)
{
cvm::fatal_error ("Error: energy_difference() not implemented.\n");
return 0.;
}
void colvarbias_harmonic::change_configuration(std::string const &conf)
void colvarbias_harmonic::change_configuration (std::string const &conf)
{
get_keyval (conf, "forceConstant", force_k, force_k);
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
@ -317,7 +349,7 @@ cvm::real colvarbias_harmonic::update()
if (target_equil_steps == 0 || cvm::step_absolute() % target_nsteps >= target_equil_steps) {
// Start averaging after equilibration period, if requested
// Square distance normalized by square colvar width
cvm::real dist_sq = 0.0;
for (size_t i = 0; i < colvars.size(); i++) {
@ -335,7 +367,7 @@ cvm::real colvarbias_harmonic::update()
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) {
@ -363,7 +395,7 @@ cvm::real colvarbias_harmonic::update()
if (cvm::debug())
cvm::log ("Done updating the harmonic bias \""+this->name+"\".\n");
// Force and energy calculation
for (size_t i = 0; i < colvars.size(); i++) {
colvar_forces[i] =
@ -379,6 +411,15 @@ cvm::real colvarbias_harmonic::update()
colvar_centers[i]))+"\n");
}
if (b_output_acc_work) {
if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
for (size_t i = 0; i < colvars.size(); i++) {
// project forces on the calculated increments at this step
acc_work += colvar_forces[i] * centers_incr[i];
}
}
}
if (cvm::debug())
cvm::log ("Current forces for the harmonic bias \""+
this->name+"\": "+cvm::to_str (colvar_forces)+".\n");
@ -408,7 +449,7 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
return is;
}
// int id = -1;
// int id = -1;
std::string name = "";
// if ( ( (colvarparse::get_keyval (conf, "id", id, -1, colvarparse::parse_silent)) &&
// (id != this->id) ) ||
@ -442,6 +483,11 @@ std::istream & colvarbias_harmonic::read_restart (std::istream &is)
cvm::fatal_error ("Error: current stage is missing from the restart.\n");
}
if (b_output_acc_work) {
if (!get_keyval (conf, "accumulatedWork", acc_work))
cvm::fatal_error ("Error: accumulatedWork is missing from the restart.\n");
}
is >> brace;
if (brace != "}") {
cvm::fatal_error ("Error: corrupt restart information for harmonic bias \""+
@ -484,9 +530,61 @@ std::ostream & colvarbias_harmonic::write_restart (std::ostream &os)
<< stage << "\n";
}
if (b_output_acc_work) {
os << " accumulatedWork " << acc_work << "\n";
}
os << " }\n"
<< "}\n\n";
return os;
}
std::ostream & colvarbias_harmonic::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_harmonic::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;
}

86
lib/colvars/colvarbias.h
View File

@ -14,7 +14,7 @@ public:
/// Name of this bias
std::string name;
/// Add a new collective variable to this bias
void add_colvar (std::string const &cv_name);
@ -35,7 +35,7 @@ public:
void communicate_forces();
/// \brief Constructor
///
///
/// The constructor of the colvarbias base class is protected, so
/// that it can only be called from inherited classes
colvarbias (std::string const &conf, char const *key);
@ -52,6 +52,13 @@ public:
/// Write the bias configuration to a restart file
virtual std::ostream & write_restart (std::ostream &os) = 0;
/// Write a label to the trajectory file (comment line)
virtual std::ostream & write_traj_label (std::ostream &os);
/// Output quantities such as the bias energy to the trajectory file
virtual std::ostream & write_traj (std::ostream &os);
protected:
/// \brief Pointers to collective variables to which the bias is
@ -62,10 +69,12 @@ protected:
/// \brief Current forces from this bias to the colvars
std::vector<colvarvalue> colvar_forces;
/// \brief Current energy of this bias (colvar_forces should be
/// obtained by deriving this)
/// \brief Current energy of this bias (colvar_forces should be obtained by deriving this)
cvm::real bias_energy;
/// Whether to write the current bias energy from this bias to the trajectory file
bool b_output_energy;
/// \brief Whether this bias has already accumulated information
/// (when relevant)
bool has_data;
@ -94,11 +103,17 @@ public:
/// Write the bias configuration to a restart file
virtual std::ostream & write_restart (std::ostream &os);
/// Write a label to the trajectory file (comment line)
virtual std::ostream & write_traj_label (std::ostream &os);
/// Output quantities such as the bias energy to the trajectory file
virtual std::ostream & write_traj (std::ostream &os);
/// \brief Constructor
colvarbias_harmonic (std::string const &conf, char const *key);
/// Destructor
virtual inline ~colvarbias_harmonic() {}
virtual ~colvarbias_harmonic();
protected:
@ -109,27 +124,9 @@ protected:
/// \brief Restraint centers without wrapping or constraints applied
std::vector<colvarvalue> colvar_centers_raw;
/// \brief Restraint force constant
cvm::real force_k;
/// \brief Moving target?
bool b_chg_centers;
/// \brief Changing force constant?
bool b_chg_force_k;
/// \brief Restraint force constant (target value)
cvm::real target_force_k;
/// \brief Equilibration steps for restraint FE calculation through TI
cvm::real target_equil_steps;
/// \brief Restraint force constant (starting value)
cvm::real starting_force_k;
/// \brief Lambda-schedule for custom varying force constant
std::vector<cvm::real> lambda_schedule;
/// \brief New restraint centers
std::vector<colvarvalue> target_centers;
@ -137,12 +134,41 @@ protected:
/// (or stage) towards the new values (calculated from target_nsteps)
std::vector<colvarvalue> centers_incr;
/// Whether to write the current restraint centers to the trajectory file
bool b_output_centers;
/// Whether to write the current accumulated work to the trajectory file
bool b_output_acc_work;
/// \brief Accumulated work
cvm::real acc_work;
/// \brief Restraint force constant
cvm::real force_k;
/// \brief Changing force constant?
bool b_chg_force_k;
/// \brief Restraint force constant (target value)
cvm::real target_force_k;
/// \brief Restraint force constant (starting value)
cvm::real starting_force_k;
/// \brief Lambda-schedule for custom varying force constant
std::vector<cvm::real> lambda_schedule;
/// \brief Exponent for varying the force constant
cvm::real force_k_exp;
/// \brief Number of steps required to reach the target force constant
/// or restraint centers
size_t target_nsteps;
/// \brief Intermediate quantity to compute the restraint free energy
/// (in TI, would be the accumulating FE derivative)
cvm::real restraint_FE;
/// \brief Equilibration steps for restraint FE calculation through TI
cvm::real target_equil_steps;
/// \brief Number of stages over which to perform the change
/// If zero, perform a continuous change
@ -150,10 +176,10 @@ protected:
/// \brief Number of current stage of the perturbation
int stage;
/// \brief Intermediate quantity to compute the restraint free energy
/// (in TI, would be the accumulating FE derivative)
cvm::real restraint_FE;
/// \brief Number of steps required to reach the target force constant
/// or restraint centers
size_t target_nsteps;
};

60
lib/colvars/colvarbias_abf.cpp
View File

@ -15,7 +15,7 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
{
if (cvm::temperature() == 0.0)
cvm::log ("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");
// ************* parsing general ABF options ***********************
get_keyval (conf, "applyBias", apply_bias, true);
@ -32,7 +32,7 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
}
get_keyval (conf, "fullSamples", full_samples, 200);
if ( full_samples <= 1 ) full_samples = 1;
if ( full_samples <= 1 ) full_samples = 1;
min_samples = full_samples / 2;
// full_samples - min_samples >= 1 is guaranteed
@ -79,7 +79,21 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
}
// Here we could check for orthogonality of the Cartesian coordinates
// and make it just a warning if some parameter is set?
// and make it just a warning if some parameter is set?
}
if (get_keyval (conf, "maxForce", max_force)) {
if (max_force.size() != colvars.size()) {
cvm::fatal_error ("Error: Number of parameters to maxForce does not match number of colvars.");
}
for (size_t i=0; i<colvars.size(); i++) {
if (max_force[i] < 0.0) {
cvm::fatal_error ("Error: maxForce should be non-negative.");
}
}
cap_force = true;
} else {
cap_force = false;
}
bin.assign (colvars.size(), 0);
@ -96,7 +110,7 @@ colvarbias_abf::colvarbias_abf (std::string const &conf, char const *key)
if ( input_prefix.size() > 0 ) {
read_gradients_samples ();
}
cvm::log ("Finished ABF setup.\n");
}
@ -114,6 +128,9 @@ colvarbias_abf::~colvarbias_abf()
}
delete [] force;
if (cvm::n_abf_biases > 0)
cvm::n_abf_biases -= 1;
}
@ -125,7 +142,7 @@ cvm::real colvarbias_abf::update()
if (cvm::debug()) cvm::log ("Updating ABF bias " + this->name);
if (cvm::step_relative() == 0) {
// At first timestep, do only:
// initialization stuff (file operations relying on n_abf_biases
// compute current value of colvars
@ -158,7 +175,7 @@ cvm::real colvarbias_abf::update()
}
// save bin for next timestep
force_bin = bin;
force_bin = bin;
// Reset biasing forces from previous timestep
for (size_t i=0; i<colvars.size(); i++) {
@ -176,19 +193,25 @@ cvm::real colvarbias_abf::update()
fact = ( count < min_samples) ? 0.0 :
(cvm::real (count - min_samples)) / (cvm::real (full_samples - min_samples));
}
const cvm::real * grad = &(gradients->value (bin));
if ( fact != 0.0 ) {
if ( (colvars.size() == 1) && colvars[0]->periodic_boundaries() ) {
// Enforce a zero-mean bias on periodic, 1D coordinates
colvar_forces[0].real_value += fact * (grad[0] / cvm::real (count) - gradients->average ());
// in other words: boundary condition is that the biasing potential is periodic
colvar_forces[0].real_value = fact * (grad[0] / cvm::real (count) - gradients->average ());
} else {
for (size_t i=0; i<colvars.size(); i++) {
// subtracting the mean force (opposite of the FE gradient) means adding the gradient
colvar_forces[i].real_value += fact * grad[i] / cvm::real (count);
// without .real_value, the above would do (cheap) runtime type checking
colvar_forces[i].real_value = fact * grad[i] / cvm::real (count);
}
}
if (cap_force) {
for (size_t i=0; i<colvars.size(); i++) {
if ( colvar_forces[i].real_value * colvar_forces[i].real_value > max_force[i] * max_force[i] ) {
colvar_forces[i].real_value = (colvar_forces[i].real_value > 0 ? max_force[i] : -1.0 * max_force[i]);
}
}
}
}
@ -203,7 +226,7 @@ cvm::real colvarbias_abf::update()
// otherwise, backup and replace
write_gradients_samples (output_prefix + ".hist", (cvm::step_absolute() > 0));
}
return 0.0; // TODO compute bias energy whenever possible (i.e. 1D with updateBias off)
return 0.0;
}
@ -250,7 +273,7 @@ void colvarbias_abf::read_gradients_samples ()
samples_in_name = input_prefix[i] + ".count";
gradients_in_name = input_prefix[i] + ".grad";
// For user-provided files, the per-bias naming scheme may not apply
std::ifstream is;
cvm::log ("Reading sample count from " + samples_in_name + " and gradients from " + gradients_in_name);
@ -272,7 +295,7 @@ void colvarbias_abf::read_gradients_samples ()
std::ostream & colvarbias_abf::write_restart (std::ostream& os)
{
std::ios::fmtflags flags (os.flags ());
std::ios::fmtflags flags (os.flags ());
os.setf(std::ios::fmtflags (0), std::ios::floatfield); // default floating-point format
os << "abf {\n"
@ -325,7 +348,7 @@ std::istream & colvarbias_abf::read_restart (std::istream& is)
if ( name == "" ) {
cvm::fatal_error ("Error: \"abf\" block in the restart file has no name.\n");
}
if ( !(is >> key) || !(key == "samples")) {
cvm::log ("Error: in reading restart configuration for ABF bias \""+
this->name+"\" at position "+
@ -381,7 +404,7 @@ colvarbias_histogram::colvarbias_histogram (std::string const &conf, char const
bin.assign (colvars.size(), 0);
out_name = cvm::output_prefix + "." + this->name + ".dat";
cvm::log ("Histogram will be written to file " + out_name);
cvm::log ("Histogram will be written to file " + out_name);
cvm::log ("Finished histogram setup.\n");
}
@ -395,6 +418,9 @@ colvarbias_histogram::~colvarbias_histogram()
delete grid;
grid = NULL;
}
if (cvm::n_histo_biases > 0)
cvm::n_histo_biases -= 1;
}
/// Update the grid
@ -452,7 +478,7 @@ std::istream & colvarbias_histogram::read_restart (std::istream& is)
cvm::fatal_error ("Error: \"histogram\" block in the restart file "
"has no name.\n");
}
if ( !(is >> key) || !(key == "grid")) {
cvm::log ("Error: in reading restart configuration for histogram \""+
this->name+"\" at position "+

6
lib/colvars/colvarbias_abf.h
View File

@ -46,6 +46,10 @@ private:
bool b_history_files;
size_t history_freq;
/// Cap applied biasing force?
bool cap_force;
std::vector<cvm::real> max_force;
// Internal data and methods
std::vector<int> bin, force_bin;
@ -84,7 +88,7 @@ private:
std::vector<int> bin;
std::string out_name;
int output_freq;
int output_freq;
void write_grid ();
std::ofstream grid_os; /// Stream for writing grid to disk

72
lib/colvars/colvarbias_meta.cpp
View File

@ -54,7 +54,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
get_keyval (conf, "multipleReplicas", b_replicas, false);
if (b_replicas)
comm = multiple_replicas;
else
else
comm = single_replica;
}
@ -76,7 +76,8 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
}
get_keyval (conf, "keepHills", keep_hills, false);
get_keyval (conf, "dumpFreeEnergyFile", dump_fes, true);
if (! get_keyval (conf, "writeFreeEnergyFile", dump_fes, true))
get_keyval (conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
get_keyval (conf, "saveFreeEnergyFile", dump_fes_save, false);
for (size_t i = 0; i < colvars.size(); i++) {
@ -113,7 +114,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
"when using more than one replica.\n");
get_keyval (conf, "replicasRegistry",
replicas_registry_file,
replicas_registry_file,
(this->name+".replicas.registry.txt"));
get_keyval (conf, "replicaUpdateFrequency",
@ -171,7 +172,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
// if this replica was not included yet, we should generate a
// new record for it: but first, we write this replica's files,
// for the others to read
// open the "hills" buffer file
replica_hills_os.open (replica_hills_file.c_str());
if (!replica_hills_os.good())
@ -188,7 +189,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
// if we're running without grids, use a growing list of "hills" files
// otherwise, just one state file and one "hills" file as buffer
std::ofstream list_os (replica_list_file.c_str(),
std::ofstream list_os (replica_list_file.c_str(),
(use_grids ? std::ios::trunc : std::ios::app));
if (! list_os.good())
cvm::fatal_error ("Error: in opening file \""+
@ -232,7 +233,7 @@ colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
cvm::log("Well-tempered metadynamics is used.\n");
cvm::log("The bias temperature is "+cvm::to_str(bias_temperature)+".\n");
}
if (cvm::debug())
cvm::log ("Done initializing the metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+".\n");
@ -258,6 +259,9 @@ colvarbias_meta::~colvarbias_meta()
if (hills_traj_os.good())
hills_traj_os.close();
if (cvm::n_meta_biases > 0)
cvm::n_meta_biases -= 1;
}
@ -266,7 +270,7 @@ colvarbias_meta::~colvarbias_meta()
// Hill management member functions
// **********************************************************************
std::list<colvarbias_meta::hill>::const_iterator
std::list<colvarbias_meta::hill>::const_iterator
colvarbias_meta::create_hill (colvarbias_meta::hill const &h)
{
hill_iter const hills_end = hills.end();
@ -324,7 +328,7 @@ colvarbias_meta::delete_hill (hill_iter &h)
}
if (hills_traj_os.good()) {
// output to the trajectory
// output to the trajectory
hills_traj_os << "# DELETED this hill: "
<< (hills.back()).output_traj()
<< "\n";
@ -459,9 +463,9 @@ cvm::real colvarbias_meta::update()
cvm::real const hills_energy_sum_here = hills_energy->value(curr_bin);
cvm::real const exp_weight = std::exp(-hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill (hill ((hill_weight*exp_weight), colvars, hill_width));
} else {
} else {
create_hill (hill (hill_weight, colvars, hill_width));
}
}
break;
case multiple_replicas:
@ -470,9 +474,9 @@ cvm::real colvarbias_meta::update()
cvm::real const hills_energy_sum_here = hills_energy->value(curr_bin);
cvm::real const exp_weight = std::exp(-hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
create_hill (hill ((hill_weight*exp_weight), colvars, hill_width, replica_id));
} else {
} else {
create_hill (hill (hill_weight, colvars, hill_width, replica_id));
}
}
if (replica_hills_os.good()) {
replica_hills_os << hills.back();
} else {
@ -591,11 +595,11 @@ cvm::real colvarbias_meta::update()
calc_hills_force (ic, new_hills_begin, hills.end(), colvar_forces);
}
if (cvm::debug())
if (cvm::debug())
cvm::log ("Hills energy = "+cvm::to_str (bias_energy)+
", hills forces = "+cvm::to_str (colvar_forces)+".\n");
if (cvm::debug())
if (cvm::debug())
cvm::log ("Metadynamics bias \""+this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
": adding the forces from the other replicas.\n");
@ -611,7 +615,7 @@ cvm::real colvarbias_meta::update()
replicas[ir]->hills.end(),
colvar_forces);
}
if (cvm::debug())
if (cvm::debug())
cvm::log ("Hills energy = "+cvm::to_str (bias_energy)+
", hills forces = "+cvm::to_str (colvar_forces)+".\n");
}
@ -641,7 +645,7 @@ void colvarbias_meta::calc_hills (colvarbias_meta::hill_iter h_first,
}
for (hill_iter h = h_first; h != h_last; h++) {
// compute the gaussian exponent
cvm::real cv_sqdev = 0.0;
for (size_t i = 0; i < colvars.size(); i++) {
@ -684,8 +688,8 @@ void colvarbias_meta::calc_hills_force (size_t const &i,
if (h->value() == 0.0) continue;
colvarvalue const &center = h->centers[i];
cvm::real const half_width = 0.5 * h->widths[i];
forces[i].real_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
forces[i].real_value +=
( h->weight() * h->value() * (0.5 / (half_width*half_width)) *
(colvars[i]->dist2_lgrad (x, center)).real_value );
}
break;
@ -993,7 +997,7 @@ void colvarbias_meta::read_replica_files()
}
// (re)read the state file if necessary
if ( (! (replicas[ir])->has_data) ||
if ( (! (replicas[ir])->has_data) ||
(! (replicas[ir])->replica_state_file_in_sync) ) {
cvm::log ("Metadynamics bias \""+this->name+"\""+
@ -1013,11 +1017,11 @@ void colvarbias_meta::read_replica_files()
}
is.close();
}
// now read the hills added after writing the state file
if ((replicas[ir])->replica_hills_file.size()) {
if (cvm::debug())
if (cvm::debug())
cvm::log ("Metadynamics bias \""+this->name+"\""+
": checking for new hills from replica \""+
(replicas[ir])->replica_id+"\" in the file \""+
@ -1064,7 +1068,7 @@ void colvarbias_meta::read_replica_files()
"\" at position "+
cvm::to_str ((replicas[ir])->replica_hills_file_pos)+".\n");
// test whether this is the end of the file
// test whether this is the end of the file
is.seekg (0, std::ios::end);
if (is.tellg() > (replicas[ir])->replica_hills_file_pos+1) {
(replicas[ir])->update_status++;
@ -1108,7 +1112,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
size_t const start_pos = is.tellg();
if (comm == single_replica) {
// if using a multiple replicas scheme, output messages
// if using a multiple replicas scheme, output messages
// are printed before and after calling this function
cvm::log ("Restarting metadynamics bias \""+this->name+"\""+
".\n");
@ -1118,7 +1122,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
!(is >> brace) || !(brace == "{") ||
!(is >> colvarparse::read_block ("configuration", conf)) ) {
if (comm == single_replica)
if (comm == single_replica)
cvm::log ("Error: in reading restart configuration for metadynamics bias \""+
this->name+"\""+
((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
@ -1239,7 +1243,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
is.clear();
is.seekg (hills_energy_gradients_pos, std::ios::beg);
grids_from_restart_file = false;
if (!rebin_grids) {
if (!rebin_grids) {
if (hills_energy_backup == NULL)
cvm::fatal_error ("Error: couldn't read the free energy gradients grid for metadynamics bias \""+
this->name+"\""+
@ -1283,7 +1287,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
// read the hills explicitly written (if there are any)
while (read_hill (is)) {
if (cvm::debug())
if (cvm::debug())
cvm::log ("Read a previously saved hill under the "
"metadynamics bias \""+
this->name+"\", created at step "+
@ -1364,7 +1368,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
hills.erase (hills.begin(), old_hills_end);
hills_off_grid.erase (hills_off_grid.begin(), old_hills_off_grid_end);
}
has_data = true;
if (comm != single_replica) {
@ -1372,7 +1376,7 @@ std::istream & colvarbias_meta::read_restart (std::istream& is)
}
return is;
}
}
std::istream & colvarbias_meta::read_hill (std::istream &is)
@ -1404,7 +1408,7 @@ std::istream & colvarbias_meta::read_hill (std::istream &is)
std::vector<colvarvalue> h_centers (colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
h_centers[i].type ((colvars[i]->value()).type());
h_centers[i].type ((colvars[i]->value()).type());
}
{
// it is safer to read colvarvalue objects one at a time;
@ -1421,7 +1425,7 @@ std::istream & colvarbias_meta::read_hill (std::istream &is)
get_keyval (data, "widths", h_widths,
std::vector<cvm::real> (colvars.size(), (std::sqrt (2.0 * PI) / 2.0)),
parse_silent);
std::string h_replica = "";
if (comm != single_replica) {
get_keyval (data, "replicaID", h_replica, replica_id, parse_silent);
@ -1517,7 +1521,7 @@ std::ostream & colvarbias_meta::write_restart (std::ostream& os)
}
return os;
}
}
void colvarbias_meta::write_pmf()
@ -1527,7 +1531,7 @@ void colvarbias_meta::write_pmf()
pmf->create();
std::string fes_file_name_prefix (cvm::output_prefix);
if ((cvm::n_meta_biases > 1) || (cvm::n_abf_biases > 0)) {
// if this is not the only free energy integrator, append
// this bias's name, to distinguish it from the output of the other
@ -1598,7 +1602,7 @@ void colvarbias_meta::write_replica_state_file()
cvm::fatal_error ("Error: in opening file \""+
replica_state_file+"\" for writing.\n");
rep_state_os.setf (std::ios::scientific, std::ios::floatfield);
rep_state_os.setf (std::ios::scientific, std::ios::floatfield);
rep_state_os << "\n"
<< "metadynamics {\n"
<< " configuration {\n"
@ -1672,7 +1676,7 @@ std::string colvarbias_meta::hill::output_traj()
<< std::setw (cvm::en_width) << W << "\n";
return os.str();
}
}
std::ostream & operator << (std::ostream &os, colvarbias_meta::hill const &h)

14
lib/colvars/colvarbias_meta.h
View File

@ -33,7 +33,7 @@ public:
/// Destructor
virtual ~colvarbias_meta();
virtual cvm::real update();
virtual std::istream & read_restart (std::istream &is);
@ -84,7 +84,7 @@ protected:
std::istream & read_hill (std::istream &is);
/// \brief step present in a state file
///
///
/// When using grids and reading state files containing them
/// (multiple replicas), this is used to check whether a hill is
/// newer or older than the grids
@ -147,10 +147,10 @@ protected:
/// time steps, appending the step number to each file
bool dump_fes_save;
/// \brief Whether to use well-tempered metadynamics
bool well_tempered;
/// \brief Whether to use well-tempered metadynamics
bool well_tempered;
/// \brief Biasing temperature in well-tempered metadynamics
/// \brief Biasing temperature in well-tempered metadynamics
cvm::real bias_temperature;
/// \brief Try to read the restart information by allocating new
@ -282,7 +282,7 @@ public:
centers[i] = cv[i]->value();
widths[i] = cv[i]->width * hill_width;
}
if (cvm::debug())
if (cvm::debug())
cvm::log ("New hill, applied to "+cvm::to_str (cv.size())+
" collective variables, with centers "+
cvm::to_str (centers)+", widths "+
@ -322,7 +322,7 @@ public:
/// Destructor
inline ~hill()
{}
/// Get the energy
inline cvm::real energy()
{

4
lib/colvars/colvarcomp.cpp
View File

@ -39,7 +39,7 @@ colvar::cvc::cvc (std::string const &conf)
}
void colvar::cvc::parse_group (std::string const &conf,
void colvar::cvc::parse_group (std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional)
@ -120,7 +120,7 @@ void colvar::cvc::debug_gradients (cvm::atom_group &group)
for (size_t id = 0; id < 3; id++) {
// (re)read original positions
group.read_positions();
// change one coordinate
// change one coordinate
group[ia].pos[id] += cvm::debug_gradients_step_size;
// (re)do the fit (if defined)
if (group.b_center || group.b_rotate) {

153
lib/colvars/colvarcomp.h
View File

@ -1,6 +1,16 @@
#ifndef COLVARCOMP_H
#define COLVARCOMP_H
// Declaration of colvar::cvc base class and derived ones.
//
// Future cvc's could be declared on additional header files.
// After the declaration of a new derived class, its metric
// functions must be reimplemented as well.
// If the new cvc has no symmetry or periodicity,
// this can be done straightforwardly by using the macro:
// simple_scalar_dist_functions (derived_class)
#include <fstream>
#include <cmath>
@ -40,7 +50,7 @@
/// 2. add a call to the parser in colvar.C, within the function colvar::colvar() \par
/// 3. declare the class in colvarcomp.h \par
/// 4. implement the class in one of the files colvarcomp_*.C
///
///
/// </b>
/// The cvm::atom and cvm::atom_group classes are available to
/// transparently communicate with the simulation program. However,
@ -58,7 +68,7 @@ public:
std::string name;
/// \brief Description of the type of collective variable
///
///
/// Normally this string is set by the parent \link colvar \endlink
/// object within its constructor, when all \link cvc \endlink
/// objects are initialized; therefore the main "config string"
@ -94,7 +104,7 @@ public:
/// \brief Within the constructor, make a group parse its own
/// options from the provided configuration string
void parse_group (std::string const &conf,
void parse_group (std::string const &conf,
char const *group_key,
cvm::atom_group &group,
bool optional = false);
@ -164,7 +174,7 @@ public:
/// \brief Square distance between x1 and x2 (can be redefined to
/// transparently implement constraints, symmetries and
/// periodicities)
///
///
/// colvar::cvc::dist2() and the related functions are
/// declared as "const" functions, but not "static", because
/// additional parameters defining the metrics (e.g. the
@ -182,7 +192,7 @@ public:
/// to provide a gradient which is compatible with the constraint,
/// i.e. already deprived of its component normal to the constraint
/// hypersurface.
///
///
/// Finally, another useful application, if you are performing very
/// many operations with these functions, could be to override the
/// \link colvarvalue \endlink member functions and access directly
@ -591,7 +601,7 @@ protected:
std::vector<cvm::atom_pos> ref_pos;
/// Geometric center of the reference coordinates
cvm::rvector 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;
@ -691,7 +701,7 @@ protected:
/// \brief Compute system force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
public:
/// Initialize by parsing the configuration
@ -759,7 +769,7 @@ public:
static cvm::real switching_function (cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |(A1-A2)*(r0_vec)^-|1 \param r0_vec
@ -808,7 +818,7 @@ public:
static cvm::real switching_function (cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
virtual cvm::real dist2 (colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad (colvarvalue const &x1,
@ -822,7 +832,7 @@ public:
/// \brief Colvar component: hydrogen bond, defined as the product of
/// a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol))
/// (colvarvalue::type_scalar type, range [0:1])
class colvar::h_bond
class colvar::h_bond
: public colvar::cvc
{
protected:
@ -887,7 +897,7 @@ public:
// alpha_dihedrals();
// virtual inline ~alpha_dihedrals() {}
// virtual void calc_value();
// virtual void calc_gradients();
// virtual void calc_gradients();
// virtual void apply_force (colvarvalue const &force);
// virtual cvm::real dist2 (colvarvalue const &x1,
// colvarvalue const &x2) const;
@ -921,7 +931,7 @@ protected:
/// List of hydrogen bonds
std::vector<h_bond *> hb;
/// Contribution of the hb terms
/// Contribution of the hb terms
cvm::real hb_coeff;
public:
@ -1140,6 +1150,62 @@ public:
};
// metrics functions for cvc implementations
// simple definitions of the distance functions; these are useful only
// for optimization (the type check performed in the default
// colvarcomp functions is skipped)
// definitions assuming the scalar type
#define simple_scalar_dist_functions(TYPE) \
\
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return 2.0 * (x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x2, x1); \
} \
\
inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x1, x2); \
} \
\
simple_scalar_dist_functions (distance)
// NOTE: distance_z has explicit functions, see below
simple_scalar_dist_functions (distance_xy)
simple_scalar_dist_functions (distance_inv)
simple_scalar_dist_functions (angle)
simple_scalar_dist_functions (coordnum)
simple_scalar_dist_functions (selfcoordnum)
simple_scalar_dist_functions (h_bond)
simple_scalar_dist_functions (gyration)
simple_scalar_dist_functions (inertia)
simple_scalar_dist_functions (inertia_z)
simple_scalar_dist_functions (rmsd)
simple_scalar_dist_functions (orientation_angle)
simple_scalar_dist_functions (tilt)
simple_scalar_dist_functions (eigenvector)
// simple_scalar_dist_functions (alpha_dihedrals)
simple_scalar_dist_functions (alpha_angles)
simple_scalar_dist_functions (dihedPC)
// metrics functions for cvc implementations with a periodicity
inline cvm::real colvar::dihedral::dist2 (colvarvalue const &x1,
@ -1177,12 +1243,12 @@ inline void colvar::dihedral::wrap (colvarvalue &x) const
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
}
return;
}
@ -1222,68 +1288,16 @@ inline void colvar::spin_angle::wrap (colvarvalue &x) const
if ((x.real_value - wrap_center) >= 180.0) {
x.real_value -= 360.0;
return;
}
}
if ((x.real_value - wrap_center) < -180.0) {
x.real_value += 360.0;
return;
}
}
return;
}
// simple definitions of the distance functions; these are useful only
// for optimization (the type check performed in the default
// colvarcomp functions is skipped)
// definitions assuming the scalar type
#define simple_scalar_dist_functions(TYPE) \
\
inline cvm::real colvar::TYPE::dist2 (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return (x1.real_value - x2.real_value)*(x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_lgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return 2.0 * (x1.real_value - x2.real_value); \
} \
\
inline colvarvalue colvar::TYPE::dist2_rgrad (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x2, x1); \
} \
\
inline cvm::real colvar::TYPE::compare (colvarvalue const &x1, \
colvarvalue const &x2) const \
{ \
return this->dist2_lgrad (x1, x2); \
} \
\
simple_scalar_dist_functions (distance)
// NOTE: distance_z has explicit functions, see below
simple_scalar_dist_functions (distance_xy)
simple_scalar_dist_functions (distance_inv)
simple_scalar_dist_functions (angle)
simple_scalar_dist_functions (coordnum)
simple_scalar_dist_functions (selfcoordnum)
simple_scalar_dist_functions (h_bond)
simple_scalar_dist_functions (gyration)
simple_scalar_dist_functions (inertia)
simple_scalar_dist_functions (inertia_z)
simple_scalar_dist_functions (rmsd)
simple_scalar_dist_functions (orientation_angle)
simple_scalar_dist_functions (tilt)
simple_scalar_dist_functions (eigenvector)
// simple_scalar_dist_functions (alpha_dihedrals)
simple_scalar_dist_functions (alpha_angles)
simple_scalar_dist_functions (dihedPC)
// Projected distance
// Differences should always be wrapped around 0 (ignoring wrap_center)
@ -1422,9 +1436,6 @@ inline cvm::real colvar::orientation::compare (colvarvalue const &x1,
}
#endif

4
lib/colvars/colvarcomp_angles.cpp
View File

@ -77,7 +77,7 @@ void colvar::angle::calc_gradients()
{
cvm::real const cos_theta = (r21*r23)/(r21l*r23l);
cvm::real const dxdcos = -1.0 / std::sqrt (1.0 - cos_theta*cos_theta);
dxdr1 = (180.0/PI) * dxdcos *
(1.0/r21l) * ( r23/r23l + (-1.0) * cos_theta * r21/r21l );
@ -246,7 +246,7 @@ void colvar::dihedral::calc_gradients()
cvm::real rA = A.norm();
cvm::rvector B = cvm::rvector::outer (r23, r34);
cvm::real rB = B.norm();
cvm::rvector C = cvm::rvector::outer (r23, A);
cvm::rvector C = cvm::rvector::outer (r23, A);
cvm::real rC = C.norm();
cvm::real const cos_phi = (A*B)/(rA*rB);

67
lib/colvars/colvarcomp_coordnums.cpp
View File

@ -72,11 +72,14 @@ cvm::real colvar::coordnum::switching_function (cvm::rvector const &r0_vec,
colvar::coordnum::coordnum (std::string const &conf)
: distance (conf), b_anisotropic (false), b_group2_center_only (false)
{
{
function_type = "coordnum";
x.type (colvarvalue::type_scalar);
// group1 and group2 are already initialized by distance()
if (group1.b_dummy)
cvm::fatal_error ("Error: only group2 is allowed to be a dummy atom\n");
// need to specify this explicitly because the distance() constructor
// has set it to true
@ -105,7 +108,7 @@ colvar::coordnum::coordnum (std::string const &conf)
cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n");
}
get_keyval (conf, "group2CenterOnly", b_group2_center_only, false);
get_keyval (conf, "group2CenterOnly", b_group2_center_only, group2.b_dummy);
}
@ -121,18 +124,10 @@ void colvar::coordnum::calc_value()
{
x.real_value = 0.0;
// these are necessary: for each atom, gradients are summed together
// by multiple calls to switching_function()
group1.reset_atoms_data();
group2.reset_atoms_data();
group1.read_positions();
group2.read_positions();
if (b_group2_center_only) {
// create a fake atom to hold the group2 com coordinates
cvm::atom group2_com_atom (group2[0]);
cvm::atom group2_com_atom;
group2_com_atom.pos = group2.center_of_mass();
if (b_anisotropic) {
@ -165,9 +160,10 @@ void colvar::coordnum::calc_gradients()
if (b_group2_center_only) {
// create a fake atom to hold the group2 com coordinates
cvm::atom group2_com_atom (group2[0]);
cvm::atom group2_com_atom;
group2_com_atom.pos = group2.center_of_mass();
if (b_anisotropic) {
for (cvm::atom_iter ai1 = group1.begin(); ai1 != group1.end(); ai1++)
switching_function<true> (r0_vec, en, ed, *ai1, group2_com_atom);
@ -288,14 +284,6 @@ colvar::h_bond::~h_bond()
void colvar::h_bond::calc_value()
{
// this is necessary, because switching_function() will sum the new
// gradient to the current one
acceptor.reset_data();
donor.reset_data();
acceptor.read_position();
donor.read_position();
x.real_value = colvar::coordnum::switching_function<false> (r0, en, ed, acceptor, donor);
}
@ -315,40 +303,11 @@ void colvar::h_bond::apply_force (colvarvalue const &force)
}
// Self-coordination number for a group
template<bool calculate_gradients>
cvm::real colvar::selfcoordnum::switching_function (cvm::real const &r0,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance (A1.pos, A2.pos);
cvm::real const l2 = diff.norm2()/(r0*r0);
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow (l2, en2);
cvm::real const xd = std::pow (l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
colvar::selfcoordnum::selfcoordnum (std::string const &conf)
: distance (conf, false)
{
{
function_type = "selfcoordnum";
x.type (colvarvalue::type_scalar);
@ -379,13 +338,9 @@ void colvar::selfcoordnum::calc_value()
{
x.real_value = 0.0;
// for each atom, gradients are summed by multiple calls to switching_function()
group1.reset_atoms_data();
group1.read_positions();
for (size_t i = 0; i < group1.size() - 1; i++)
for (size_t j = i + 1; j < group1.size(); j++)
x.real_value += switching_function<false> (r0, en, ed, group1[i], group1[j]);
x.real_value += colvar::coordnum::switching_function<false> (r0, en, ed, group1[i], group1[j]);
}
@ -393,7 +348,7 @@ void colvar::selfcoordnum::calc_gradients()
{
for (size_t i = 0; i < group1.size() - 1; i++)
for (size_t j = i + 1; j < group1.size(); j++)
switching_function<true> (r0, en, ed, group1[i], group1[j]);
colvar::coordnum::switching_function<true> (r0, en, ed, group1[i], group1[j]);
}
void colvar::selfcoordnum::apply_force (colvarvalue const &force)

68
lib/colvars/colvarcomp_distances.cpp
View File

@ -113,7 +113,7 @@ void colvar::distance_vec::calc_value()
}
void colvar::distance_vec::calc_gradients()
{
{
// gradients are not stored: a 3x3 matrix for each atom would be
// needed to store just the identity matrix
}
@ -140,7 +140,7 @@ colvar::distance_z::distance_z (std::string const &conf)
// TODO detect PBC from MD engine (in simple cases)
// and then update period in real time
if (period != 0.0)
b_periodic = true;
b_periodic = true;
if ((wrap_center != 0.0) && (period == 0.0)) {
cvm::fatal_error ("Error: wrapAround was defined in a distanceZ component,"
@ -153,7 +153,7 @@ colvar::distance_z::distance_z (std::string const &conf)
atom_groups.push_back (&ref1);
// this group is optional
parse_group (conf, "ref2", ref2, true);
if (ref2.size()) {
atom_groups.push_back (&ref2);
cvm::log ("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
@ -522,7 +522,7 @@ colvar::gyration::gyration (std::string const &conf)
cvm::log ("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
} else {
atoms.b_center = true;
atoms.ref_pos.assign (1, cvm::rvector (0.0, 0.0, 0.0));
atoms.ref_pos.assign (1, cvm::atom_pos (0.0, 0.0, 0.0));
}
x.type (colvarvalue::type_scalar);
@ -700,7 +700,7 @@ colvar::rmsd::rmsd (std::string const &conf)
parse_group (conf, "atoms", atoms);
atom_groups.push_back (&atoms);
if (atoms.b_dummy)
if (atoms.b_dummy)
cvm::fatal_error ("Error: \"atoms\" cannot be a dummy atom.");
if (atoms.ref_pos_group != NULL) {
@ -732,7 +732,7 @@ colvar::rmsd::rmsd (std::string const &conf)
std::string ref_pos_col;
double ref_pos_col_value;
if (get_keyval (conf, "refPositionsCol", ref_pos_col, std::string (""))) {
// if provided, use PDB column to select coordinates
bool found = get_keyval (conf, "refPositionsColValue", ref_pos_col_value, 0.0);
@ -771,7 +771,7 @@ colvar::rmsd::rmsd (std::string const &conf)
}
}
void colvar::rmsd::calc_value()
{
// rotational-translational fit is handled by the atom group
@ -813,9 +813,9 @@ void colvar::rmsd::calc_force_invgrads()
{
atoms.read_system_forces();
ft.real_value = 0.0;
// Note: gradient square norm is 1/N_atoms
for (size_t ia = 0; ia < atoms.size(); ia++) {
ft.real_value += atoms[ia].grad * atoms[ia].system_force;
}
@ -832,7 +832,7 @@ void colvar::rmsd::calc_Jacobian_derivative()
// gradient of the rotation matrix
cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat;
// gradients of products of 2 quaternion components
// gradients of products of 2 quaternion components
cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23;
for (size_t ia = 0; ia < atoms.size(); ia++) {
@ -850,15 +850,15 @@ void colvar::rmsd::calc_Jacobian_derivative()
g23 = (atoms.rot.q)[2]*dq[3] + (atoms.rot.q)[3]*dq[2];
// Gradient of the rotation matrix wrt current Cartesian position
grad_rot_mat[0][0] = -2.0 * (g22 + g33);
grad_rot_mat[1][0] = 2.0 * (g12 + g03);
grad_rot_mat[2][0] = 2.0 * (g13 - g02);
grad_rot_mat[0][1] = 2.0 * (g12 - g03);
grad_rot_mat[1][1] = -2.0 * (g11 + g33);
grad_rot_mat[2][1] = 2.0 * (g01 + g23);
grad_rot_mat[0][2] = 2.0 * (g02 + g13);
grad_rot_mat[1][2] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);
grad_rot_mat[0][0] = -2.0 * (g22 + g33);
grad_rot_mat[1][0] = 2.0 * (g12 + g03);
grad_rot_mat[2][0] = 2.0 * (g13 - g02);
grad_rot_mat[0][1] = 2.0 * (g12 - g03);
grad_rot_mat[1][1] = -2.0 * (g11 + g33);
grad_rot_mat[2][1] = 2.0 * (g01 + g23);
grad_rot_mat[0][2] = 2.0 * (g02 + g13);
grad_rot_mat[1][2] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);
cvm::atom_pos &y = ref_pos[ia];
@ -991,7 +991,7 @@ colvar::eigenvector::eigenvector (std::string const &conf)
"and eigenvector must be defined.\n");
}
cvm::rvector eig_center (0.0, 0.0, 0.0);
cvm::atom_pos eig_center (0.0, 0.0, 0.0);
for (size_t i = 0; i < atoms.size(); i++) {
eig_center += eigenvec[i];
}
@ -1053,7 +1053,7 @@ colvar::eigenvector::eigenvector (std::string const &conf)
}
}
void colvar::eigenvector::calc_value()
{
x.real_value = 0.0;
@ -1087,7 +1087,7 @@ void colvar::eigenvector::calc_force_invgrads()
{
atoms.read_system_forces();
ft.real_value = 0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
ft.real_value += eigenvec_invnorm2 * atoms[ia].grad *
atoms[ia].system_force;
@ -1101,10 +1101,10 @@ void colvar::eigenvector::calc_Jacobian_derivative()
cvm::matrix2d <cvm::rvector, 3, 3> grad_rot_mat;
cvm::quaternion &quat0 = atoms.rot.q;
// gradients of products of 2 quaternion components
// gradients of products of 2 quaternion components
cvm::rvector g11, g22, g33, g01, g02, g03, g12, g13, g23;
cvm::atom_pos x_relative;
cvm::atom_pos x_relative;
cvm::real sum = 0.0;
for (size_t ia = 0; ia < atoms.size(); ia++) {
@ -1126,15 +1126,15 @@ void colvar::eigenvector::calc_Jacobian_derivative()
// Gradient of the inverse rotation matrix wrt current Cartesian position
// (transpose of the gradient of the direct rotation)
grad_rot_mat[0][0] = -2.0 * (g22 + g33);
grad_rot_mat[0][1] = 2.0 * (g12 + g03);
grad_rot_mat[0][2] = 2.0 * (g13 - g02);
grad_rot_mat[1][0] = 2.0 * (g12 - g03);
grad_rot_mat[1][1] = -2.0 * (g11 + g33);
grad_rot_mat[1][2] = 2.0 * (g01 + g23);
grad_rot_mat[2][0] = 2.0 * (g02 + g13);
grad_rot_mat[2][1] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);
grad_rot_mat[0][0] = -2.0 * (g22 + g33);
grad_rot_mat[0][1] = 2.0 * (g12 + g03);
grad_rot_mat[0][2] = 2.0 * (g13 - g02);
grad_rot_mat[1][0] = 2.0 * (g12 - g03);
grad_rot_mat[1][1] = -2.0 * (g11 + g33);
grad_rot_mat[1][2] = 2.0 * (g01 + g23);
grad_rot_mat[2][0] = 2.0 * (g02 + g13);
grad_rot_mat[2][1] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);
for (size_t i = 0; i < 3; i++) {
for (size_t j = 0; j < 3; j++) {
@ -1143,7 +1143,7 @@ void colvar::eigenvector::calc_Jacobian_derivative()
}
}
jd.real_value = sum * std::sqrt (eigenvec_invnorm2);
jd.real_value = sum * std::sqrt (eigenvec_invnorm2);
}

16
lib/colvars/colvarcomp_protein.cpp
View File

@ -122,7 +122,7 @@ void colvar::alpha_angles::calc_value()
if (theta.size()) {
cvm::real const theta_norm =
cvm::real const theta_norm =
(1.0-hb_coeff) / cvm::real (theta.size());
for (size_t i = 0; i < theta.size(); i++) {
@ -162,7 +162,7 @@ void colvar::alpha_angles::calc_value()
void colvar::alpha_angles::calc_gradients()
{
for (size_t i = 0; i < theta.size(); i++)
for (size_t i = 0; i < theta.size(); i++)
(theta[i])->calc_gradients();
for (size_t i = 0; i < hb.size(); i++)
@ -175,9 +175,9 @@ void colvar::alpha_angles::apply_force (colvarvalue const &force)
if (theta.size()) {
cvm::real const theta_norm =
cvm::real const theta_norm =
(1.0-hb_coeff) / cvm::real (theta.size());
for (size_t i = 0; i < theta.size(); i++) {
cvm::real const t = ((theta[i])->value().real_value-theta_ref)/theta_tol;
@ -185,10 +185,10 @@ void colvar::alpha_angles::apply_force (colvarvalue const &force)
(1.0 - std::pow (t, (int) 4)) );
cvm::real const dfdt =
1.0/(1.0 - std::pow (t, (int) 4)) *
1.0/(1.0 - std::pow (t, (int) 4)) *
( (-2.0 * t) + (-1.0*f)*(-4.0 * std::pow (t, (int) 3)) );
(theta[i])->apply_force (theta_norm *
(theta[i])->apply_force (theta_norm *
dfdt * (1.0/theta_tol) *
force.real_value );
}
@ -216,7 +216,7 @@ void colvar::alpha_angles::apply_force (colvarvalue const &force)
// of this cvc (alpha)
// This is true of all cvcs with sub-cvcs, and those
// that do not calculate explicit gradients
// SO: we need a flag giving the availability of
// SO: we need a flag giving the availability of
// atomic gradients
colvar::dihedPC::dihedPC (std::string const &conf)
: cvc (conf)
@ -260,7 +260,7 @@ colvar::dihedPC::dihedPC (std::string const &conf)
std::string vecFileName;
int vecNumber;
if (get_keyval (conf, "vectorFile", vecFileName, vecFileName)) {
get_keyval (conf, "vectorNumber", vecNumber, 0);
get_keyval (conf, "vectorNumber", vecNumber, 0);
if (vecNumber < 1)
cvm::fatal_error ("A positive value of vectorNumber is required.");

4
lib/colvars/colvarcomp_rotations.cpp
View File

@ -74,7 +74,7 @@ colvar::orientation::orientation (std::string const &conf)
}
colvar::orientation::orientation()
: cvc ()
{
@ -160,7 +160,7 @@ void colvar::orientation_angle::calc_value()
void colvar::orientation_angle::calc_gradients()
{
cvm::real const dxdq0 =
( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
( ((rot.q).q0 * (rot.q).q0 < 1.0) ?
((180.0 / PI) * (-2.0) / std::sqrt (1.0 - ((rot.q).q0 * (rot.q).q0))) :
0.0 );

4
lib/colvars/colvargrid.cpp
View File

@ -141,7 +141,7 @@ void colvar_grid_gradient::write_1D_integral (std::ostream &os)
{
cvm::real bin, min, integral;
std::vector<cvm::real> int_vals;
os << "# xi A(xi)\n";
if ( cv.size() != 1 ) {
@ -162,7 +162,7 @@ void colvar_grid_gradient::write_1D_integral (std::ostream &os)
}
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix), bin += 1.0 ) {
if (samples) {
size_t const samples_here = samples->value (ix);
if (samples_here)

54
lib/colvars/colvargrid.h
View File

@ -266,11 +266,11 @@ public:
}
{
{
cvm::real nbins = ( upper_boundaries[i].real_value -
lower_boundaries[i].real_value ) / widths[i];
int nbins_round = (int)(nbins+0.5);
if (std::fabs (nbins - cvm::real (nbins_round)) > 1.0E-10) {
cvm::log ("Warning: grid interval ("+
cvm::to_str (lower_boundaries[i], cvm::cv_width, cvm::cv_prec)+" - "+
@ -284,7 +284,7 @@ public:
if (cvm::debug())
cvm::log ("Number of points is "+cvm::to_str ((int) nbins_round)+
" for the colvar no. "+cvm::to_str (i+1)+".\n");
nx_i.push_back (nbins_round);
}
@ -336,7 +336,7 @@ public:
{
return lower_boundaries[i].real_value + widths[i] * (0.5 + i_bin);
}
/// \brief Same as the standard version, but uses different parameters
inline colvarvalue bin_to_value_scalar (int const &i_bin,
colvarvalue const &new_offset,
@ -349,7 +349,7 @@ public:
inline void set_value (std::vector<int> const &ix,
T const &t,
size_t const &imult = 0)
{
{
data[this->address (ix)+imult] = t;
has_data = true;
}
@ -367,7 +367,7 @@ public:
/// \brief Add a constant to all elements (fast loop)
inline void add_constant (T const &t)
{
for (size_t i = 0; i < nt; i++)
for (size_t i = 0; i < nt; i++)
data[i] += t;
has_data = true;
}
@ -375,11 +375,11 @@ public:
/// \brief Multiply all elements by a scalar constant (fast loop)
inline void multiply_constant (cvm::real const &a)
{
for (size_t i = 0; i < nt; i++)
for (size_t i = 0; i < nt; i++)
data[i] *= a;
}
/// \brief Get the bin indices corresponding to the provided values of
/// the colvars
inline std::vector<int> const get_colvars_index (std::vector<colvarvalue> const &values) const
@ -432,7 +432,7 @@ public:
/// \brief Add data from another grid of the same type
///
///
/// Note: this function maps other_grid inside this one regardless
/// of whether it fits or not.
void map_grid (colvar_grid<T> const &other_grid)
@ -482,11 +482,11 @@ public:
if (other_grid.multiplicity() != this->multiplicity())
cvm::fatal_error ("Error: trying to sum togetehr two grids with values of "
"different multiplicity.\n");
if (scale_factor != 1.0)
if (scale_factor != 1.0)
for (size_t i = 0; i < data.size(); i++) {
data[i] += scale_factor * other_grid.data[i];
}
else
else
// skip multiplication if possible
for (size_t i = 0; i < data.size(); i++) {
data[i] += other_grid.data[i];
@ -571,30 +571,30 @@ public:
std::ostream & write_params (std::ostream &os)
{
os << "grid_parameters {\n n_colvars " << nd << "\n";
os << " lower_boundaries ";
for (size_t i = 0; i < nd; i++)
for (size_t i = 0; i < nd; i++)
os << " " << lower_boundaries[i];
os << "\n";
os << " upper_boundaries ";
for (size_t i = 0; i < nd; i++)
for (size_t i = 0; i < nd; i++)
os << " " << upper_boundaries[i];
os << "\n";
os << " widths ";
for (size_t i = 0; i < nd; i++)
for (size_t i = 0; i < nd; i++)
os << " " << widths[i];
os << "\n";
os << " sizes ";
for (size_t i = 0; i < nd; i++)
for (size_t i = 0; i < nd; i++)
os << " " << nx[i];
os << "\n";
os << "}\n";
return os;
}
}
bool parse_params (std::string const &conf)
@ -648,9 +648,9 @@ public:
{
for (size_t i = 0; i < nd; i++) {
if ( (std::sqrt (cv[i]->dist2 (cv[i]->lower_boundary,
lower_boundaries[i])) > 1.0E-10) ||
lower_boundaries[i])) > 1.0E-10) ||
(std::sqrt (cv[i]->dist2 (cv[i]->upper_boundary,
upper_boundaries[i])) > 1.0E-10) ||
upper_boundaries[i])) > 1.0E-10) ||
(std::sqrt (cv[i]->dist2 (cv[i]->width,
widths[i])) > 1.0E-10) ) {
cvm::fatal_error ("Error: restart information for a grid is "
@ -669,11 +669,11 @@ public:
// matter: boundaries should be EXACTLY the same (otherwise,
// map_grid() should be used)
if ( (std::fabs (other_grid.lower_boundaries[i] -
lower_boundaries[i]) > 1.0E-10) ||
lower_boundaries[i]) > 1.0E-10) ||
(std::fabs (other_grid.upper_boundaries[i] -
upper_boundaries[i]) > 1.0E-10) ||
upper_boundaries[i]) > 1.0E-10) ||
(std::fabs (other_grid.widths[i] -
widths[i]) > 1.0E-10) ||
widths[i]) > 1.0E-10) ||
(data.size() != other_grid.data.size()) ) {
cvm::fatal_error ("Error: inconsistency between "
"two grids that are supposed to be equal, "
@ -681,7 +681,7 @@ public:
}
}
}
/// \brief Write the grid data without labels, as they are
/// represented in memory
@ -714,7 +714,7 @@ public:
std::istream & read_raw (std::istream &is)
{
size_t const start_pos = is.tellg();
for (std::vector<int> ix = new_index(); index_ok (ix); incr (ix)) {
for (size_t imult = 0; imult < mult; imult++) {
T new_value;
@ -845,7 +845,7 @@ std::istream & read_multicol (std::istream &is, bool add = false)
if ( !(is >> x) ) end_of_file = true;
bin[i] = value_to_bin_scalar (x, i);
}
if (end_of_file) break;
if (end_of_file) break;
for (size_t imult = 0; imult < mult; imult++) {
is >> new_value[imult];
@ -904,7 +904,7 @@ public:
++(data[this->address (ix)]);
}
/// \brief Get the binned count indexed by ix from the newly read data
/// \brief Get the binned count indexed by ix from the newly read data
inline size_t const & new_count (std::vector<int> const &ix,
size_t const &imult = 0)
{
@ -993,7 +993,7 @@ public:
A0 += data[address (ix)];
grad[n] = 0.5 * (A1 - A0) / widths[n];
}
return grad;
return grad;
}
/// \brief Return the value of the function at ix divided by its

153
lib/colvars/colvarmodule.cpp
View File

@ -9,14 +9,14 @@
colvarmodule::colvarmodule (char const *config_filename,
colvarproxy *proxy_in)
{
{
// pointer to the proxy object
if (proxy == NULL) {
proxy = proxy_in;
parse = new colvarparse();
} else {
cvm::fatal_error ("Error: trying to allocate twice the collective "
"variable module.\n");
cvm::fatal_error ("Error: trying to allocate the collective "
"variable module twice.\n");
}
cvm::log (cvm::line_marker);
@ -44,6 +44,11 @@ colvarmodule::colvarmodule (char const *config_filename,
config_s.close();
}
std::string index_file_name;
if (parse->get_keyval (conf, "indexFile", index_file_name)) {
read_index_file (index_file_name.c_str());
}
parse->get_keyval (conf, "analysis", b_analysis, false);
parse->get_keyval (conf, "debugGradientsStepSize", debug_gradients_step_size, 1.0e-07,
@ -80,12 +85,10 @@ colvarmodule::colvarmodule (char const *config_filename,
std::string (output_prefix+".colvars.state") :
std::string ("colvars.state"))+"\".\n");
cv_traj_name =
cv_traj_name =
(output_prefix.size() ?
std::string (output_prefix+".colvars.traj") :
std::string ("colvars.traj"));
cvm::log ("The trajectory file will be \""+
cv_traj_name+"\".\n");
if (cv_traj_freq) {
// open trajectory file
@ -94,6 +97,8 @@ colvarmodule::colvarmodule (char const *config_filename,
"\".\n");
cv_traj_os.open (cv_traj_name.c_str(), std::ios::app);
} else {
cvm::log ("Writing to colvar trajectory file \""+cv_traj_name+
"\".\n");
proxy->backup_file (cv_traj_name.c_str());
cv_traj_os.open (cv_traj_name.c_str(), std::ios::out);
}
@ -135,7 +140,7 @@ colvarmodule::colvarmodule (char const *config_filename,
}
std::istream & colvarmodule::read_restart (std::istream &is)
std::istream & colvarmodule::read_restart (std::istream &is)
{
{
// read global restart information
@ -192,7 +197,7 @@ void colvarmodule::init_colvars (std::string const &conf)
(colvars.back())->check_keywords (colvar_conf, "colvar");
cvm::decrease_depth();
} else {
cvm::log ("Warning: \"colvar\" keyword found without any configuration.\n");
cvm::log ("Warning: \"colvar\" keyword found without any configuration.\n");
}
colvar_conf = "";
}
@ -347,13 +352,13 @@ void colvarmodule::calc() {
}
// calculate collective variables and their gradients
if (cvm::debug())
if (cvm::debug())
cvm::log ("Calculating collective variables.\n");
cvm::increase_depth();
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
(*cvi)->calc();
(*cvi)->calc();
}
cvm::decrease_depth();
@ -365,7 +370,7 @@ void colvarmodule::calc() {
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
total_bias_energy += (*bi)->update();
total_bias_energy += (*bi)->update();
}
cvm::decrease_depth();
@ -376,12 +381,12 @@ void colvarmodule::calc() {
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
(*cvi)->reset_bias_force();
(*cvi)->reset_bias_force();
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
(*bi)->communicate_forces();
(*bi)->communicate_forces();
}
cvm::decrease_depth();
@ -393,12 +398,12 @@ void colvarmodule::calc() {
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
(*cvi)->analyse();
(*cvi)->analyse();
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
(*bi)->analyse();
(*bi)->analyse();
}
cvm::decrease_depth();
}
@ -426,7 +431,7 @@ void colvarmodule::calc() {
cvi != colvars.end();
cvi++) {
if ((*cvi)->tasks[colvar::task_gradients])
(*cvi)->communicate_forces();
(*cvi)->communicate_forces();
}
cvm::decrease_depth();
@ -442,7 +447,7 @@ void colvarmodule::calc() {
if (!write_restart (restart_out_os))
cvm::fatal_error ("Error: in writing restart file.\n");
restart_out_os.close();
}
}
}
// write trajectory file, if needed
@ -471,15 +476,20 @@ void colvarmodule::calc() {
if ((cvm::step_absolute() % (cv_traj_freq * 1000)) == 0 || cvm::step_relative() == 0) {
cv_traj_os << "# " << cvm::wrap_string ("step", cvm::it_width-2)
<< " ";
if (cvm::debug())
if (cvm::debug())
cv_traj_os.flush();
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
cvi++) {
(*cvi)->write_traj_label (cv_traj_os);
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
(*bi)->write_traj_label (cv_traj_os);
}
cv_traj_os << "\n";
if (cvm::debug())
if (cvm::debug())
cv_traj_os.flush();
}
cvm::decrease_depth();
@ -494,13 +504,18 @@ void colvarmodule::calc() {
cvi++) {
(*cvi)->write_traj (cv_traj_os);
}
for (std::vector<colvarbias *>::iterator bi = biases.begin();
bi != biases.end();
bi++) {
(*bi)->write_traj (cv_traj_os);
}
cv_traj_os << "\n";
if (cvm::debug())
cv_traj_os.flush();
}
cvm::decrease_depth();
if (restart_out_freq) {
if (restart_out_freq) {
// flush the trajectory file if we are at the restart frequency
if ( (cvm::step_relative() > 0) &&
((cvm::step_absolute() % restart_out_freq) == 0) ) {
@ -527,7 +542,7 @@ void colvarmodule::analyze()
cvi != colvars.end();
cvi++) {
cvm::increase_depth();
(*cvi)->analyse();
(*cvi)->analyse();
cvm::decrease_depth();
}
@ -536,12 +551,20 @@ void colvarmodule::analyze()
bi != biases.end();
bi++) {
cvm::increase_depth();
(*bi)->analyse();
(*bi)->analyse();
cvm::decrease_depth();
}
}
void colvarmodule::setup()
{
// loop over all components of all colvars to reset masses of all groups
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end(); cvi++) {
(*cvi)->setup();
}
}
colvarmodule::~colvarmodule()
{
@ -565,7 +588,7 @@ colvarmodule::~colvarmodule()
delete parse;
proxy = NULL;
}
}
void colvarmodule::write_output_files()
@ -590,7 +613,7 @@ void colvarmodule::write_output_files()
(*cvi)->write_output_files();
}
cvm::decrease_depth();
// do not close to avoid problems with multiple NAMD runs
cv_traj_os.flush();
}
@ -631,7 +654,7 @@ bool colvarmodule::read_traj (char const *traj_filename,
continue;
} else {
} else {
if ((it % 1000) == 0)
std::cerr << "Reading from trajectory, step = " << it
@ -721,6 +744,55 @@ void cvm::exit (std::string const &message)
}
void cvm::read_index_file (char const *filename)
{
std::ifstream is (filename);
if (!is.good())
fatal_error ("Error: in opening index file \""+
std::string (filename)+"\".\n");
// std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
// std::list<std::vector<int> >::iterator lists_i = cvm::index_groups.begin();
while (is.good()) {
char open, close;
std::string group_name;
if ( (is >> open) && (open == '[') &&
(is >> group_name) &&
(is >> close) && (close == ']') ) {
cvm::index_group_names.push_back (group_name);
cvm::index_groups.push_back (std::vector<int> ());
} else {
cvm::fatal_error ("Error: in parsing index file \""+
std::string (filename)+"\".\n");
}
int atom_number = 1;
size_t pos = is.tellg();
while ( (is >> atom_number) && (atom_number > 0) ) {
(cvm::index_groups.back()).push_back (atom_number);
pos = is.tellg();
}
is.clear();
is.seekg (pos, std::ios::beg);
std::string delim;
if ( (is >> delim) && (delim == "[") ) {
// new group
is.clear();
is.seekg (pos, std::ios::beg);
} else {
break;
}
}
cvm::log ("The following index groups were read from the index file \""+
std::string (filename)+"\":\n");
std::list<std::string>::iterator names_i = cvm::index_group_names.begin();
std::list<std::vector<int> >::iterator lists_i = cvm::index_groups.begin();
for ( ; names_i != cvm::index_group_names.end() ; names_i++, lists_i++) {
cvm::log (" "+(*names_i)+" ("+cvm::to_str (lists_i->size())+" atoms).\n");
}
}
// static pointers
std::vector<colvar *> colvarmodule::colvars;
@ -741,6 +813,8 @@ size_t colvarmodule::cv_traj_freq = 0;
size_t colvarmodule::depth = 0;
bool colvarmodule::b_analysis = false;
cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-04;
std::list<std::string> colvarmodule::index_group_names;
std::list<std::vector<int> > colvarmodule::index_groups;
// file name prefixes
@ -827,7 +901,7 @@ std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
std::string ("euler")) ) {
// parse the Euler angles
char sep;
cvm::real phi, theta, psi;
if ( !(is >> sep) || !(sep == '(') ||
@ -846,7 +920,7 @@ std::istream & operator >> (std::istream &is, colvarmodule::quaternion &q)
// parse the quaternion components
is.seekg (start_pos, std::ios::beg);
is.seekg (start_pos, std::ios::beg);
char sep;
if ( !(is >> sep) || !(sep == '(') ||
!(is >> q.q0) || !(is >> sep) || !(sep == ',') ||
@ -932,15 +1006,13 @@ cvm::quaternion::position_derivative_inner (cvm::rvector const &pos,
// Calculate the optimal rotation between two groups, and implement it
// as a quaternion. The method is the one documented in: Coutsias EA,
// Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput
// Chem. 25(15):1849-57 (2004) DOI: 10.1002/jcc.20110 PubMed: 15376254
void colvarmodule::rotation::build_matrix (std::vector<cvm::atom_pos> const &pos1,
std::vector<cvm::atom_pos> const &pos2,
matrix2d<cvm::real, 4, 4> &S)
@ -959,7 +1031,7 @@ void colvarmodule::rotation::build_matrix (std::vector<cvm::atom_pos> const &pos
C.zx() += pos1[i].z * pos2[i].x;
C.zy() += pos1[i].z * pos2[i].y;
C.zz() += pos1[i].z * pos2[i].z;
}
}
// build the "overlap" matrix, whose eigenvectors are stationary
// points of the RMSD in the space of rotations
@ -1068,11 +1140,12 @@ void colvarmodule::rotation::calc_optimal_rotation
if (q_old.norm2() > 0.0) {
q.match (q_old);
if (q_old.inner (q) < (1.0 - crossing_threshold)) {
cvm::log ("Warning: discontinuous rotation!\n");
cvm::log ("Warning: one molecular orientation has changed by more than "+
cvm::to_str (crossing_threshold)+": discontinuous rotation ?\n");
}
}
q_old = q;
if (cvm::debug()) {
if (b_debug_gradients) {
cvm::log ("L0 = "+cvm::to_str (L0, cvm::cv_width, cvm::cv_prec)+
@ -1143,8 +1216,8 @@ void colvarmodule::rotation::calc_optimal_rotation
for (size_t i = 0; i < 4; i++) {
for (size_t j = 0; j < 4; j++) {
dq0_1[p] +=
(Q1[i] * ds_1[i][j] * Q0[j]) / (L0-L1) * Q1[p] +
(Q2[i] * ds_1[i][j] * Q0[j]) / (L0-L2) * Q2[p] +
(Q1[i] * ds_1[i][j] * Q0[j]) / (L0-L1) * Q1[p] +
(Q2[i] * ds_1[i][j] * Q0[j]) / (L0-L2) * Q2[p] +
(Q3[i] * ds_1[i][j] * Q0[j]) / (L0-L3) * Q3[p];
}
}
@ -1193,15 +1266,15 @@ void colvarmodule::rotation::calc_optimal_rotation
for (size_t i = 0; i < 4; i++) {
for (size_t j = 0; j < 4; j++) {
dq0_2[p] +=
(Q1[i] * ds_2[i][j] * Q0[j]) / (L0-L1) * Q1[p] +
(Q2[i] * ds_2[i][j] * Q0[j]) / (L0-L2) * Q2[p] +
(Q1[i] * ds_2[i][j] * Q0[j]) / (L0-L1) * Q1[p] +
(Q2[i] * ds_2[i][j] * Q0[j]) / (L0-L2) * Q2[p] +
(Q3[i] * ds_2[i][j] * Q0[j]) / (L0-L3) * Q3[p];
}
}
}
if (cvm::debug()) {
if (b_debug_gradients) {
matrix2d<cvm::real, 4, 4> S_new;
@ -1216,7 +1289,7 @@ void colvarmodule::rotation::calc_optimal_rotation
// diagonalize the new overlap matrix
for (size_t i = 0; i < 4; i++) {
for (size_t j = 0; j < 4; j++) {
S_new[i][j] +=
S_new[i][j] +=
colvarmodule::debug_gradients_step_size * ds_2[i][j][comp];
}
}

48
lib/colvars/colvarmodule.h
View File

@ -2,16 +2,16 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2013-04-17"
#define COLVARS_VERSION "2013-06-19"
#endif
#ifndef COLVARS_DEBUG
#define COLVARS_DEBUG false
#endif
/// \file colvarmodule.h
/// \file colvarmodule.h
/// \brief Collective variables main module
///
///
/// This file declares the main class for defining and manipulating
/// collective variables: there should be only one instance of this
/// class, because several variables are made static (i.e. they are
@ -40,7 +40,7 @@ class colvarproxy;
/// Class to control the collective variables calculation. An object
/// (usually one) of this class is spawned from the MD program,
/// containing all i/o routines and general interface.
///
///
/// At initialization, the colvarmodule object creates a proxy object
/// to provide a transparent interface between the MD program and the
/// child objects
@ -54,7 +54,7 @@ private:
public:
friend class colvarproxy;
/// Defining an abstract real number allows to switch precision
typedef double real;
/// Residue identifier
@ -147,7 +147,7 @@ public:
/// \brief Number of histograms initialized (no limit on the
/// number)
static size_t n_histo_biases;
/// \brief Whether debug output should be enabled (compile-time option)
static inline bool debug()
{
@ -157,8 +157,9 @@ public:
/// \brief Constructor \param config_name Configuration file name
/// \param restart_name (optional) Restart file name
colvarmodule (char const *config_name,
colvarmodule (char const *config_name,
colvarproxy *proxy_in);
/// Destructor
~colvarmodule();
@ -168,6 +169,11 @@ public:
/// Initialize collective variable biases
void init_biases (std::string const &conf);
/// Re-initialize data at the beginning of a run. For use with
/// MD codes that can change system parameters like atom masses
/// between run commands.
void setup();
/// Load new configuration for the given bias -
/// currently works for harmonic (force constant and/or centers)
void change_configuration (std::string const &bias_name, std::string const &conf);
@ -194,16 +200,16 @@ public:
bool read_traj (char const *traj_filename,
size_t traj_read_begin,
size_t traj_read_end);
/// Get the pointer of a colvar from its name (returns NULL if not found)
static colvar * colvar_p (std::string const &name);
/// Quick conversion of an object to a string
template<typename T> static std::string to_str (T const &x,
template<typename T> static std::string to_str (T const &x,
size_t const &width = 0,
size_t const &prec = 0);
/// Quick conversion of a vector of objects to a string
template<typename T> static std::string to_str (std::vector<T> const &x,
template<typename T> static std::string to_str (std::vector<T> const &x,
size_t const &width = 0,
size_t const &prec = 0);
@ -247,10 +253,10 @@ public:
/// \brief Time step of MD integrator (fs)
static real dt();
/// Request calculation of system force from MD engine
static void request_system_force();
/// Print a message to the main log
static void log (std::string const &message);
@ -278,7 +284,7 @@ public:
/// \brief Get the closest periodic image to a reference position
/// \param pos The position to look for the closest periodic image
/// \param ref_pos (optional) The reference position
/// \param ref_pos (optional) The reference position
static void select_closest_image (atom_pos &pos,
atom_pos const &ref_pos);
@ -290,6 +296,16 @@ public:
atom_pos const &ref_pos);
/// \brief Names of groups from a Gromacs .ndx file to be read at startup
static std::list<std::string> index_group_names;
/// \brief Groups from a Gromacs .ndx file read at startup
static std::list<std::vector<int> > index_groups;
/// \brief Read a Gromacs .ndx file
static void read_index_file (char const *filename);
/// \brief Create atoms from a file \param filename name of the file
/// (usually a PDB) \param atoms array of the atoms to be allocated
/// \param pdb_field (optiona) if "filename" is a PDB file, use this
@ -371,7 +387,7 @@ std::ostream & operator << (std::ostream &os, cvm::rvector const &v);
std::istream & operator >> (std::istream &is, cvm::rvector &v);
template<typename T> std::string cvm::to_str (T const &x,
template<typename T> std::string cvm::to_str (T const &x,
size_t const &width,
size_t const &prec) {
std::ostringstream os;
@ -384,7 +400,7 @@ template<typename T> std::string cvm::to_str (T const &x,
return os.str();
}
template<typename T> std::string cvm::to_str (std::vector<T> const &x,
template<typename T> std::string cvm::to_str (std::vector<T> const &x,
size_t const &width,
size_t const &prec) {
if (!x.size()) return std::string ("");
@ -434,7 +450,7 @@ inline void cvm::request_system_force()
{
proxy->request_system_force (true);
}
inline void cvm::select_closest_image (atom_pos &pos,
atom_pos const &ref_pos)
{

34
lib/colvars/colvarparse.cpp
View File

@ -241,11 +241,11 @@ _get_keyval_vector_ (colvarvalue);
bool colvarparse::get_keyval (std::string const &conf,
char const *key,
bool &value,
bool const &def_value,
Parse_Mode const parse_mode)
bool colvarparse::get_keyval (std::string const &conf,
char const *key,
bool &value,
bool const &def_value,
Parse_Mode const parse_mode)
{
std::string data;
bool b_found = false, b_found_any = false;
@ -277,7 +277,7 @@ bool colvarparse::get_keyval (std::string const &conf,
(data == std::string ("false")) ) {
value = false;
} else
cvm::fatal_error ("Error: boolean values only are allowed "
cvm::fatal_error ("Error: boolean values only are allowed "
"for \""+std::string (key)+"\".\n");
if (parse_mode != parse_silent) {
cvm::log ("# "+std::string (key)+" = "+
@ -371,8 +371,8 @@ void colvarparse::check_keywords (std::string &conf, char const *key)
std::string uk;
std::istringstream line_is (line);
line_is >> uk;
if (cvm::debug())
cvm::log ("Checking the validity of \""+uk+"\" from line:\n" + line);
// if (cvm::debug())
// cvm::log ("Checking the validity of \""+uk+"\" from line:\n" + line);
uk = to_lower_cppstr (uk);
bool found_keyword = false;
@ -426,8 +426,8 @@ bool colvarparse::key_lookup (std::string const &conf,
colvarparse::dummy_pos = 0;
// start from the first occurrence of key
size_t pos = conf_lower.find (key, save_pos);
size_t pos = conf_lower.find (key, save_pos);
// iterate over all instances until it finds the isolated keyword
while (true) {
@ -442,7 +442,7 @@ bool colvarparse::key_lookup (std::string const &conf,
if ( std::string ("\n"+white_space+
"}").find (conf[pos-1]) ==
std::string::npos ) {
// none of the valid delimiting characters is on the left of key
// none of the valid delimiting characters is on the left of key
b_isolated_left = false;
}
}
@ -451,7 +451,7 @@ bool colvarparse::key_lookup (std::string const &conf,
if ( std::string ("\n"+white_space+
"{").find (conf[pos+key.size()]) ==
std::string::npos ) {
// none of the valid delimiting characters is on the right of key
// none of the valid delimiting characters is on the right of key
b_isolated_right = false;
}
}
@ -461,7 +461,7 @@ bool colvarparse::key_lookup (std::string const &conf,
bool const b_isolated = (b_isolated_left && b_isolated_right &&
b_not_within_block);
if (b_isolated) {
// found it
break;
@ -490,7 +490,7 @@ bool colvarparse::key_lookup (std::string const &conf,
size_t line_begin = (pl == std::string::npos) ? 0 : pos;
size_t nl = conf.find ("\n", pos);
size_t line_end = (nl == std::string::npos) ? conf.size() : nl;
std::string line (conf, line_begin, (line_end-line_begin));
std::string line (conf, line_begin, (line_end-line_begin));
size_t data_begin = (to_lower_cppstr (line)).find (key) + key.size();
data_begin = line.find_first_not_of (white_space, data_begin+1);
@ -527,9 +527,9 @@ bool colvarparse::key_lookup (std::string const &conf,
line_begin = line_end;
nl = conf.find ('\n', line_begin+1);
if (nl == std::string::npos)
if (nl == std::string::npos)
line_end = conf.size();
else
else
line_end = nl;
line.append (conf, line_begin, (line_end-line_begin));
@ -565,7 +565,7 @@ bool colvarparse::key_lookup (std::string const &conf,
// << "\n";
}
}
save_pos = line_end;
return true;

10
lib/colvars/colvarparse.h
View File

@ -53,15 +53,15 @@ public:
{}
/// How a keyword is parsed in a string
enum Parse_Mode {
enum Parse_Mode {
/// \brief (default) Read the first instance of a keyword (if
/// any), report its value, and print a warning when there is more
/// than one
parse_normal,
parse_normal,
/// \brief Like parse_normal, but don't send any message to the log
/// (useful e.g. in restart files when such messages are very
/// numerous and redundant)
parse_silent
parse_silent
};
/// \fn get_keyval bool const get_keyval (std::string const &conf,
@ -112,7 +112,7 @@ public:
std::vector<_type_> const &def_values = \
std::vector<_type_> (0, static_cast<_type_>(_def_value_)), \
Parse_Mode const parse_mode = parse_normal)
_get_keyval_vector_proto_ (int, 0);
_get_keyval_vector_proto_ (size_t, 0);
_get_keyval_vector_proto_ (std::string, std::string (""));
@ -169,7 +169,7 @@ public:
/// data (optional) holds the string provided after "key", if any
/// \param save_pos (optional) stores the position of the keyword
/// within "conf", useful when doing multiple calls \param
/// save_delimiters (optional)
/// save_delimiters (optional)
bool key_lookup (std::string const &conf,
char const *key,
std::string &data = dummy_string,

78
lib/colvars/colvarproxy.h
View File

@ -16,6 +16,12 @@ public:
/// Pointer to the instance of colvarmodule
colvarmodule *colvars;
/// Default destructor
virtual inline ~colvarproxy() {}
// **************** SYSTEM-WIDE PHYSICAL QUANTITIES ****************
/// \brief Value of the unit for atomic coordinates with respect to
/// angstroms (used by some variables for hard-coded default values)
virtual cvm::real unit_angstrom() = 0;
@ -29,21 +35,11 @@ public:
/// \brief Time step of the simulation (fs)
virtual cvm::real dt() = 0;
/// Pass restraint energy value for current timestep to MD engine
virtual void add_energy (cvm::real energy) = 0;
/// \brief Pseudo-random number with Gaussian distribution
virtual cvm::real rand_gaussian (void) = 0;
/// Tell the proxy whether system forces are needed
virtual void request_system_force (bool yesno) = 0;
/// Print a message to the main log
virtual void log (std::string const &message) = 0;
/// Print a message to the main log and exit with error code
virtual void fatal_error (std::string const &message) = 0;
/// Print a message to the main log and exit normally
virtual void exit (std::string const &message) = 0;
// **************** SIMULATION PARAMETERS ****************
/// \brief Prefix to be used for input files (restarts, not
/// configuration)
@ -59,25 +55,32 @@ public:
/// \brief Restarts will be fritten each time this number of steps has passed
virtual size_t restart_frequency() = 0;
// **************** ACCESS ATOMIC DATA ****************
/// Pass restraint energy value for current timestep to MD engine
virtual void add_energy (cvm::real energy) = 0;
/// Tell the proxy whether system forces are needed (may not always be available)
virtual void request_system_force (bool yesno) = 0;
// **************** PERIODIC BOUNDARY CONDITIONS ****************
/// \brief Get the simple distance vector between two positions
/// (with periodic boundary conditions handled transparently)
/// \brief Get the PBC-aware distance vector between two positions
virtual cvm::rvector position_distance (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) = 0;
/// \brief Get the square distance between two positions (with
/// periodic boundary conditions handled transparently)
///
/// Note: in the case of periodic boundary conditions, this provides
/// an analytical square distance (while taking the square of
/// position_distance() would produce leads to a cusp)
/// \brief Get the PBC-aware square distance between two positions;
/// may be implemented independently from position_distance() for optimization purposes
virtual cvm::real position_dist2 (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2) = 0;
cvm::atom_pos const &pos2);
/// \brief Get the closest periodic image to a reference position
/// \param pos The position to look for the closest periodic image
/// \param ref_pos The reference position
/// \param ref_pos The reference position
virtual void select_closest_image (cvm::atom_pos &pos,
cvm::atom_pos const &ref_pos) = 0;
@ -89,6 +92,18 @@ public:
cvm::atom_pos const &ref_pos);
// **************** INPUT/OUTPUT ****************
/// Print a message to the main log
virtual void log (std::string const &message) = 0;
/// Print a message to the main log and exit with error code
virtual void fatal_error (std::string const &message) = 0;
/// Print a message to the main log and exit normally
virtual void exit (std::string const &message) = 0;
/// \brief Read atom identifiers from a file \param filename name of
/// the file (usually a PDB) \param atoms array to which atoms read
/// from "filename" will be appended \param pdb_field (optiona) if
@ -97,7 +112,7 @@ public:
virtual void load_atoms (char const *filename,
std::vector<cvm::atom> &atoms,
std::string const pdb_field,
double const pdb_field_value = 0.0) = 0;
double const pdb_field_value = 0.0) {}
/// \brief Load the coordinates for a group of atoms from a file
/// (usually a PDB); if "pos" is already allocated, the number of its
@ -108,14 +123,9 @@ public:
std::string const pdb_field,
double const pdb_field_value = 0.0) = 0;
/// \brief Rename the given file, under the convention provided by
/// the MD program
virtual void backup_file (char const *filename) = 0;
/// \brief Rename the given file, before overwriting it
virtual void backup_file (char const *filename) {}
/// \brief Pseudo-random number with Gaussian distribution
virtual cvm::real rand_gaussian (void) = 0;
virtual inline ~colvarproxy() {}
};
@ -128,6 +138,12 @@ inline void colvarproxy::select_closest_images (std::vector<cvm::atom_pos> &pos,
}
}
inline cvm::real colvarproxy::position_dist2 (cvm::atom_pos const &pos1,
cvm::atom_pos const &pos2)
{
return (position_distance (pos1, pos2)).norm2();
}
#endif

74
lib/colvars/colvartypes.h
View File

@ -19,7 +19,7 @@ class colvarmodule::rvector {
public:
cvm::real x, y, z;
inline rvector()
: x (0.0), y (0.0), z (0.0)
{}
@ -55,7 +55,7 @@ public:
}
inline cvm::rvector & operator = (cvm::real const &v)
inline cvm::rvector & operator = (cvm::real const &v)
{
x = v;
y = v;
@ -63,28 +63,28 @@ public:
return *this;
}
inline void operator += (cvm::rvector const &v)
inline void operator += (cvm::rvector const &v)
{
x += v.x;
y += v.y;
z += v.z;
}
inline void operator -= (cvm::rvector const &v)
inline void operator -= (cvm::rvector const &v)
{
x -= v.x;
y -= v.y;
z -= v.z;
}
inline void operator *= (cvm::real const &v)
inline void operator *= (cvm::real const &v)
{
x *= v;
y *= v;
z *= v;
}
inline void operator /= (cvm::real const& v)
inline void operator /= (cvm::real const& v)
{
x /= v;
y /= v;
@ -113,57 +113,57 @@ public:
}
static inline cvm::rvector outer (cvm::rvector const &v1, cvm::rvector const &v2)
static inline cvm::rvector outer (cvm::rvector const &v1, cvm::rvector const &v2)
{
return cvm::rvector ( v1.y*v2.z - v2.y*v1.z,
-v1.x*v2.z + v2.x*v1.z,
v1.x*v2.y - v2.x*v1.y);
}
friend inline cvm::rvector operator - (cvm::rvector const &v)
friend inline cvm::rvector operator - (cvm::rvector const &v)
{
return cvm::rvector (-v.x, -v.y, -v.z);
}
friend inline int operator == (cvm::rvector const &v1, cvm::rvector const &v2)
friend inline int operator == (cvm::rvector const &v1, cvm::rvector const &v2)
{
return (v1.x == v2.x) && (v1.y == v2.y) && (v1.z == v2.z);
}
friend inline int operator != (cvm::rvector const &v1, cvm::rvector const &v2)
friend inline int operator != (cvm::rvector const &v1, cvm::rvector const &v2)
{
return (v1.x != v2.x) || (v1.y != v2.y) || (v1.z != v2.z);
}
friend inline cvm::rvector operator + (cvm::rvector const &v1, cvm::rvector const &v2)
friend inline cvm::rvector operator + (cvm::rvector const &v1, cvm::rvector const &v2)
{
return cvm::rvector (v1.x + v2.x, v1.y + v2.y, v1.z + v2.z);
}
friend inline cvm::rvector operator - (cvm::rvector const &v1, cvm::rvector const &v2)
friend inline cvm::rvector operator - (cvm::rvector const &v1, cvm::rvector const &v2)
{
return cvm::rvector (v1.x - v2.x, v1.y - v2.y, v1.z - v2.z);
}
friend inline cvm::real operator * (cvm::rvector const &v1, cvm::rvector const &v2)
friend inline cvm::real operator * (cvm::rvector const &v1, cvm::rvector const &v2)
{
return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z;
}
friend inline cvm::rvector operator * (cvm::real const &a, cvm::rvector const &v)
friend inline cvm::rvector operator * (cvm::real const &a, cvm::rvector const &v)
{
return cvm::rvector (a*v.x, a*v.y, a*v.z);
}
friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real const &a)
friend inline cvm::rvector operator * (cvm::rvector const &v, cvm::real const &a)
{
return cvm::rvector (a*v.x, a*v.y, a*v.z);
}
friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real const &a)
friend inline cvm::rvector operator / (cvm::rvector const &v, cvm::real const &a)
{
return cvm::rvector (v.x/a, v.y/a, v.z/a);
}
};
@ -186,7 +186,7 @@ public:
{
return length;
}
/// Default constructor
inline vector1d (T const &t = T())
{
@ -251,7 +251,7 @@ public:
return prod;
}
/// Formatted output
/// Formatted output
friend std::ostream & operator << (std::ostream &os,
vector1d<T, length> const &v)
{
@ -310,7 +310,7 @@ public:
this->alloc();
reset();
}
/// Constructor from a 2-d C array
inline matrix2d (T const **m)
{
@ -380,7 +380,7 @@ public:
// }
// }
/// Formatted output
/// Formatted output
friend std::ostream & operator << (std::ostream &os,
matrix2d<T, outer_length, inner_length> const &m)
{
@ -454,16 +454,16 @@ public:
inline cvm::real zz() const { return array[2][2]; }
/// Constructor from a 2-d C array
inline rmatrix (cvm::real const **m)
: cvm::matrix2d<cvm::real, 3, 3> (m)
inline rmatrix (cvm::real const **m)
: cvm::matrix2d<cvm::real, 3, 3> (m)
{}
/// Default constructor
inline rmatrix()
inline rmatrix()
: cvm::matrix2d<cvm::real, 3, 3>()
{}
/// Constructor component by component
/// Constructor component by component
inline rmatrix (cvm::real const &xxi,
cvm::real const &xyi,
cvm::real const &xzi,
@ -472,7 +472,7 @@ public:
cvm::real const &yzi,
cvm::real const &zxi,
cvm::real const &zyi,
cvm::real const &zzi)
cvm::real const &zzi)
: cvm::matrix2d<cvm::real, 3, 3>()
{
this->xx() = xxi;
@ -488,7 +488,7 @@ public:
/// Destructor
inline ~rmatrix()
{}
{}
/// Return the determinant
inline cvm::real determinant() const
@ -528,7 +528,7 @@ public:
};
inline cvm::rvector operator * (cvm::rmatrix const &m,
cvm::rvector const &r)
{
@ -680,7 +680,7 @@ public:
return std::sqrt (this->norm2());
}
/// Return the conjugate quaternion
/// Return the conjugate quaternion
inline cvm::quaternion conjugate() const
{
return cvm::quaternion (q0, -q1, -q2, -q3);
@ -720,7 +720,7 @@ public:
return cvm::quaternion (0.0, v.x, v.y, v.z);
}
/// Return the vector component
inline cvm::rvector get_vector() const
inline cvm::rvector get_vector() const
{
return cvm::rvector (q1, q2, q3);
}
@ -1002,11 +1002,11 @@ public:
if (q.q0 != 0.0) {
// cvm::real const x = iprod/q.q0;
cvm::real const dspindx = (180.0/PI) * 2.0 * (1.0 / (1.0 + (iprod*iprod)/(q.q0*q.q0)));
return
cvm::quaternion ( dspindx * (iprod * (-1.0) / (q.q0*q.q0)),
return
cvm::quaternion ( dspindx * (iprod * (-1.0) / (q.q0*q.q0)),
dspindx * ((1.0/q.q0) * axis.x),
dspindx * ((1.0/q.q0) * axis.y),
dspindx * ((1.0/q.q0) * axis.z));
@ -1023,11 +1023,11 @@ public:
inline cvm::real cos_theta (cvm::rvector const &axis) const
{
cvm::rvector const q_vec = q.get_vector();
cvm::real const alpha =
cvm::real const alpha =
(180.0/PI) * 2.0 * std::atan2 (axis * q_vec, q.q0);
cvm::real const cos_spin_2 = std::cos (alpha * (PI/180.0) * 0.5);
cvm::real const cos_theta_2 = ( (cos_spin_2 != 0.0) ?
cvm::real const cos_theta_2 = ( (cos_spin_2 != 0.0) ?
(q.q0 / cos_spin_2) :
(0.0) );
// cos(2t) = 2*cos(t)^2 - 1
@ -1044,7 +1044,7 @@ public:
if (q.q0 != 0.0) {
cvm::real const d_cos_theta_dq0 =
cvm::real const d_cos_theta_dq0 =
(4.0 * q.q0 / (cos_spin_2*cos_spin_2)) *
(1.0 - (iprod*iprod)/(q.q0*q.q0) / (1.0 + (iprod*iprod)/(q.q0*q.q0)));
@ -1052,7 +1052,7 @@ public:
(4.0 * q.q0 / (cos_spin_2*cos_spin_2) *
(iprod/q.q0) / (1.0 + (iprod*iprod)/(q.q0*q.q0)));
return cvm::quaternion (d_cos_theta_dq0,
return cvm::quaternion (d_cos_theta_dq0,
d_cos_theta_dqn * axis.x,
d_cos_theta_dqn * axis.y,
d_cos_theta_dqn * axis.z);

14
lib/colvars/colvarvalue.cpp
View File

@ -28,7 +28,7 @@ void colvarvalue::error_rside
cvm::fatal_error ("Trying to assign a colvar value with type \""+
type_desc[this->value_type]+"\" to one with type \""+
type_desc[vt]+"\".\n");
}
}
void colvarvalue::error_lside
(colvarvalue::Type const &vt) const
@ -36,7 +36,7 @@ void colvarvalue::error_lside
cvm::fatal_error ("Trying to use a colvar value with type \""+
type_desc[vt]+"\" as one of type \""+
type_desc[this->value_type]+"\".\n");
}
}
@ -125,7 +125,7 @@ void colvarvalue::p2leg_opt (colvarvalue const &x,
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
cvm::real const cosine =
cvm::real const cosine =
((xvi)->rvector_value * x.rvector_value) /
((xvi)->rvector_value.norm() * x.rvector_value.norm());
xvi++;
@ -167,7 +167,7 @@ void colvarvalue::p2leg_opt (colvarvalue const &x,
break;
case colvarvalue::type_vector:
while (xvi != xv_end) {
cvm::real const cosine =
cvm::real const cosine =
((xvi)->rvector_value * x.rvector_value) /
((xvi)->rvector_value.norm() * x.rvector_value.norm());
xvi++;
@ -225,11 +225,11 @@ std::istream & operator >> (std::istream &is, colvarvalue &x)
switch (x.type()) {
case colvarvalue::type_scalar:
is >> x.real_value;
is >> x.real_value;
break;
case colvarvalue::type_vector:
case colvarvalue::type_unitvector:
is >> x.rvector_value;
is >> x.rvector_value;
break;
case colvarvalue::type_quaternion:
is >> x.quaternion_value;
@ -242,7 +242,7 @@ std::istream & operator >> (std::istream &is, colvarvalue &x)
}
size_t colvarvalue::output_width (size_t const &real_width)
size_t colvarvalue::output_width (size_t const &real_width) const
{
switch (this->value_type) {
case colvarvalue::type_scalar:

24
lib/colvars/colvarvalue.h
View File

@ -37,7 +37,7 @@
/// the problem, because \link colvarvalue \endlink objects are first
/// initialized in the configuration, and the stream operation will be
/// performed only when reading restart files.
///
///
/// No problem of course with the output streams: \code os << x;
/// \endcode will print a different output according to the value of
/// colvarvalue::value_type, and the width of such output is returned
@ -92,7 +92,7 @@ public:
cvm::quaternion quaternion_value;
/// Current type of this colvarvalue object
Type value_type;
Type value_type;
static inline bool type_checking()
{
@ -146,7 +146,7 @@ public:
case type_scalar:
real_value = x.real_value;
break;
case type_vector:
case type_vector:
case type_unitvector:
rvector_value = x.rvector_value;
break;
@ -254,7 +254,7 @@ public:
/// Ensure that the two types are the same within a binary operator
void static check_types (colvarvalue const &x1, colvarvalue const &x2);
/// Undefined operation
/// Undefined operation
void undef_op() const;
/// Trying to assign this \link colvarvalue \endlink object to
@ -265,10 +265,10 @@ public:
/// with a different type to this object
void error_rside (Type const &vt) const;
///<EFBFBD>Give the number of characters required to output this
/// Give the number of characters required to output this
/// colvarvalue, given the current type assigned and the number of
/// characters for a real number
size_t output_width (size_t const &real_width);
size_t output_width (size_t const &real_width) const;
// optimized routines for operations with an array; xv and inner as
@ -324,7 +324,7 @@ inline void colvarvalue::reset()
case colvarvalue::type_notset:
default:
break;
}
}
}
@ -344,7 +344,7 @@ inline void colvarvalue::apply_constraints()
case colvarvalue::type_notset:
default:
break;
}
}
}
@ -362,7 +362,7 @@ inline cvm::real colvarvalue::norm2() const
case colvarvalue::type_notset:
default:
return 0.0;
}
}
}
@ -383,7 +383,7 @@ inline colvarvalue colvarvalue::inverse() const
case colvarvalue::type_notset:
default:
undef_op();
}
}
return colvarvalue();
}
@ -391,11 +391,11 @@ inline colvarvalue colvarvalue::inverse() const
inline colvarvalue & colvarvalue::operator = (colvarvalue const &x)
{
if (this->value_type != type_notset)
if (this->value_type != x.value_type)
if (this->value_type != x.value_type)
error_lside (x.value_type);
this->value_type = x.value_type;
switch (this->value_type) {
case colvarvalue::type_scalar:
this->real_value = x.real_value;