ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12612 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-10-07 20:30:25 +00:00
parent 3c0612815f
commit 044084847b
33 changed files with 2284 additions and 2595 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
lib/colvars/colvarbias_alb.cpp
View File

@ -13,6 +13,7 @@
colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
colvarbias(conf, key), update_calls(0), b_equilibration(true) {
size_t i;
// get the initial restraint centers
colvar_centers.resize (colvars.size());
@ -29,7 +30,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
coupling_rate.resize(colvars.size());
for (size_t i = 0; i < colvars.size(); i++) {
for (i = 0; i < colvars.size(); i++) {
colvar_centers[i].type (colvars[i]->type());
//zero moments
means[i] = ssd[i] = 0;
@ -39,7 +40,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
}
if (get_keyval (conf, "centers", colvar_centers, colvar_centers)) {
for (size_t i = 0; i < colvars.size(); i++) {
for (i = 0; i < colvars.size(); i++) {
colvar_centers[i].apply_constraints();
}
} else {
@ -52,7 +53,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
"that of collective variables.\n");
if(!get_keyval (conf, "UpdateFrequency", update_freq, 0))
cvm::fatal_error("Error: must set updateFrequency for apadtive linear bias.\n");
cvm::fatal_error("Error: must set updateFrequency for adaptive linear bias.\n");
//we split the time between updating and equilibrating
update_freq /= 2;
@ -67,21 +68,21 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
//initial guess
if(!get_keyval (conf, "forceConstant", set_coupling, set_coupling))
for(size_t i =0 ; i < colvars.size(); i++)
for(i =0 ; i < colvars.size(); i++)
set_coupling[i] = 0.;
//how we're going to increase to that point
for(size_t i = 0; i < colvars.size(); i++)
for(i = 0; i < colvars.size(); i++)
coupling_rate[i] = (set_coupling[i] - current_coupling[i]) / update_freq;
if(!get_keyval (conf, "forceRange", max_coupling_range, max_coupling_range)) {
//set to default
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
if(cvm::temperature() > 0)
max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann();
max_coupling_range[i] = 3 * cvm::temperature() * cvm::boltzmann();
else
max_coupling_range[i] = 3 * cvm::boltzmann();
max_coupling_range[i] = 3 * cvm::boltzmann();
}
}
@ -89,7 +90,7 @@ colvarbias_alb::colvarbias_alb(std::string const &conf, char const *key) :
if(!get_keyval (conf, "rateMax", max_coupling_rate, max_coupling_rate)) {
//set to default
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
max_coupling_rate[i] = max_coupling_range[i] / (10 * update_freq);
}
}
@ -123,9 +124,9 @@ cvm::real colvarbias_alb::update() {
bool finished_equil_flag = 1;
cvm::real delta;
for (size_t i = 0; i < colvars.size(); i++) {
colvar_forces[i] = -restraint_force(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
colvar_forces[i] = -1.0 * restraint_force(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
bias_energy += restraint_potential(restraint_convert_k(current_coupling[i], colvars[i]->width),
colvars[i],
colvar_centers[i]);
@ -193,7 +194,7 @@ cvm::real colvarbias_alb::update() {
ssd[i] = 0;
//stochastic if we do that update or not
if(colvars.size() == 1 || rand() < RAND_MAX / colvars.size()) {
if(colvars.size() == 1 || rand() < RAND_MAX / ((int) colvars.size())) {
coupling_accum[i] += step_size * step_size;
current_coupling[i] = set_coupling[i];
set_coupling[i] += max_coupling_range[i] / sqrt(coupling_accum[i]) * step_size;
@ -294,37 +295,38 @@ std::ostream & colvarbias_alb::write_restart (std::ostream &os)
<< " configuration {\n"
<< " name " << this->name << "\n";
os << " setCoupling ";
for(size_t i = 0; i < colvars.size(); i++) {
size_t i;
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << set_coupling[i] << "\n";
}
os << " currentCoupling ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << current_coupling[i] << "\n";
}
os << " maxCouplingRange ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << max_coupling_range[i] << "\n";
}
os << " couplingRate ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << coupling_rate[i] << "\n";
}
os << " couplingAccum ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << coupling_accum[i] << "\n";
}
os << " mean ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << means[i] << "\n";
}
os << " ssd ";
for(size_t i = 0; i < colvars.size(); i++) {
for(i = 0; i < colvars.size(); i++) {
os << std::setprecision (cvm::en_prec)
<< std::setw (cvm::en_width) << ssd[i] << "\n";
}