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Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF

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This commit is contained in:
Giacomo Fiorin
2016-10-24 17:05:47 -04:00
parent ad57a17f48
commit c243093980
3 changed files with 43 additions and 36 deletions
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20
lib/colvars/colvar.cpp
View File

@ -1144,9 +1144,9 @@ cvm::real colvar::update_forces_energy()
// For a periodic colvar, both walls may be applicable at the same time
// in which case we pick the closer one
if ( (!is_enabled(f_cv_upper_wall)) ||
(this->dist2(x, lower_wall) < this->dist2(x, upper_wall)) ) {
(this->dist2(x_reported, lower_wall) < this->dist2(x_reported, upper_wall)) ) {
cvm::real const grad = this->dist2_lgrad(x, lower_wall);
cvm::real const grad = this->dist2_lgrad(x_reported, lower_wall);
if (grad < 0.0) {
fw = -0.5 * lower_wall_k * grad;
f += fw;
@ -1157,7 +1157,7 @@ cvm::real colvar::update_forces_energy()
} else {
cvm::real const grad = this->dist2_lgrad(x, upper_wall);
cvm::real const grad = this->dist2_lgrad(x_reported, upper_wall);
if (grad > 0.0) {
fw = -0.5 * upper_wall_k * grad;
f += fw;
@ -1177,15 +1177,21 @@ cvm::real colvar::update_forces_energy()
// atoms only feel the harmonic force
// fr: bias force on extended variable (without harmonic spring), for output in trajectory
// f_ext: total force on extended variable (including harmonic spring)
// f: - initially, external biasing force
// f: - initially, external biasing force (including wall forces)
// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
fr = f;
f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
// The total force acting on the extended variable is f_ext
// This will be used in the next timestep
ft_reported = f_ext;
if (is_enabled(f_cv_subtract_applied_force)) {
// Report a "system" force without the biases on this colvar
// that is, just the spring force
ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
} else {
// The total force acting on the extended variable is f_ext
// This will be used in the next timestep
ft_reported = f_ext;
}
// leapfrog: starting from x_i, f_i, v_(i-1/2)
vr += (0.5 * dt) * f_ext / ext_mass;

57
lib/colvars/colvarbias_abf.cpp
View File

@ -80,6 +80,7 @@ int colvarbias_abf::init(std::string const &conf)
if (update_bias) {
// Request calculation of total force (which also checks for availability)
// TODO - change this to a dependency - needs ABF-specific features
if(enable(f_cvb_get_total_force)) return cvm::get_error();
}
@ -133,6 +134,10 @@ int colvarbias_abf::init(std::string const &conf)
// Data for eABF z-based estimator
if (b_extended) {
// CZAR output files for stratified eABF
get_keyval(conf, "writeCZARwindowFile", b_czar_window_file, false,
colvarparse::parse_silent);
z_bin.assign(colvars.size(), 0);
z_samples = new colvar_grid_count(colvars);
z_samples->request_actual_value();
@ -241,7 +246,7 @@ int colvarbias_abf::update()
for (size_t i = 0; i < colvars.size(); i++) {
// get total forces (lagging by 1 timestep) from colvars
// and subtract previous ABF force
// and subtract previous ABF force if necessary
update_system_force(i);
}
gradients->acc_force(force_bin, system_force);
@ -457,28 +462,30 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
if (z_gradients) {
// Write eABF-related quantities
std::string z_samples_out_name = prefix + ".zcount";
std::string z_gradients_out_name = prefix + ".zgrad";
std::string czar_gradients_out_name = prefix + ".czar";
cvm::ofstream z_samples_os;
cvm::ofstream z_gradients_os;
cvm::ofstream czar_gradients_os;
if (!append) cvm::backup_file(z_samples_out_name.c_str());
z_samples_os.open(z_samples_out_name.c_str(), mode);
if (!z_samples_os.is_open()) {
cvm::error("Error opening ABF z sample file " + z_samples_out_name + " for writing");
cvm::error("Error opening eABF z-histogram file " + z_samples_out_name + " for writing");
}
z_samples->write_multicol(z_samples_os);
z_samples_os.close();
if (!append) cvm::backup_file(z_gradients_out_name.c_str());
z_gradients_os.open(z_gradients_out_name.c_str(), mode);
if (!z_gradients_os.is_open()) {
cvm::error("Error opening ABF z gradient file " + z_gradients_out_name + " for writing");
if (b_czar_window_file) {
std::string z_gradients_out_name = prefix + ".zgrad";
cvm::ofstream z_gradients_os;
if (!append) cvm::backup_file(z_gradients_out_name.c_str());
z_gradients_os.open(z_gradients_out_name.c_str(), mode);
if (!z_gradients_os.is_open()) {
cvm::error("Error opening eABF z-gradient file " + z_gradients_out_name + " for writing");
}
z_gradients->write_multicol(z_gradients_os);
z_gradients_os.close();
}
z_gradients->write_multicol(z_gradients_os);
z_gradients_os.close();
// Calculate CZAR estimator of gradients
for (std::vector<int> ix = czar_gradients->new_index();
@ -490,6 +497,9 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
}
}
std::string czar_gradients_out_name = prefix + ".czar.grad";
cvm::ofstream czar_gradients_os;
if (!append) cvm::backup_file(czar_gradients_out_name.c_str());
czar_gradients_os.open(czar_gradients_out_name.c_str(), mode);
if (!czar_gradients_os.is_open()) {
@ -499,17 +509,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
czar_gradients_os.close();
if (colvars.size() == 1) {
std::string z_pmf_out_name = prefix + ".zpmf";
if (!append) cvm::backup_file(z_pmf_out_name.c_str());
cvm::ofstream z_pmf_os;
// Do numerical integration and output a PMF
z_pmf_os.open(z_pmf_out_name.c_str(), mode);
if (!z_pmf_os.is_open()) cvm::error("Error opening z pmf file " + z_pmf_out_name + " for writing");
z_gradients->write_1D_integral(z_pmf_os);
z_pmf_os << std::endl;
z_pmf_os.close();
std::string czar_pmf_out_name = prefix + ".czarpmf";
std::string czar_pmf_out_name = prefix + ".czar.pmf";
if (!append) cvm::backup_file(czar_pmf_out_name.c_str());
cvm::ofstream czar_pmf_os;
// Do numerical integration and output a PMF
@ -520,8 +520,6 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
czar_pmf_os.close();
}
}
return;
}
@ -559,7 +557,7 @@ void colvarbias_abf::read_gradients_samples()
std::ifstream is;
cvm::log("Reading sample count from " + samples_in_name + " and gradients from " + gradients_in_name);
cvm::log("Reading sample count from " + samples_in_name + " and gradient from " + gradients_in_name);
is.open(samples_in_name.c_str());
if (!is.is_open()) cvm::error("Error opening ABF samples file " + samples_in_name + " for reading");
samples->read_multicol(is, true);
@ -572,17 +570,18 @@ void colvarbias_abf::read_gradients_samples()
is.close();
if (z_gradients) {
cvm::log("Reading z sample count from " + z_samples_in_name + " and z gradients from " + z_gradients_in_name);
// Read eABF z-averaged data for CZAR
cvm::log("Reading z-histogram from " + z_samples_in_name + " and z-gradient from " + z_gradients_in_name);
is.clear();
is.open(z_samples_in_name.c_str());
if (!is.is_open()) cvm::error("Error opening ABF z samples file " + z_samples_in_name + " for reading");
if (!is.is_open()) cvm::error("Error opening eABF z-histogram file " + z_samples_in_name + " for reading");
z_samples->read_multicol(is, true);
is.close();
is.clear();
is.open(z_gradients_in_name.c_str());
if (!is.is_open()) cvm::error("Error opening ABF z gradient file " + z_gradients_in_name + " for reading");
if (!is.is_open()) cvm::error("Error opening eABF z-gradient file " + z_gradients_in_name + " for reading");
z_gradients->read_multicol(is, true);
is.close();
}

2
lib/colvars/colvarbias_abf.h
View File

@ -40,6 +40,8 @@ private:
int output_freq;
/// Write combined files with a history of all output data?
bool b_history_files;
/// Write CZAR output file for stratified eABF (.zgrad)
bool b_czar_window_file;
size_t history_freq;
/// Cap applied biasing force?