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

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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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81
lib/colvars/colvar.cpp
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@ -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++;
}