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

Update Colvars to version 2017-10-11

Browse Source 
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
This commit is contained in:
Giacomo Fiorin
2017-10-13 13:25:02 -04:00
parent a973c65d67
commit 3e89b270fd
34 changed files with 1795 additions and 275 deletions
Download Patch File Download Diff File Expand all files Collapse all files

61
lib/colvars/colvarbias_abf.cpp
View File

@ -14,6 +14,8 @@
colvarbias_abf::colvarbias_abf(char const *key)
: colvarbias(key),
b_UI_estimator(false),
b_CZAR_estimator(false),
system_force(NULL),
gradients(NULL),
samples(NULL),
@ -159,6 +161,7 @@ int colvarbias_abf::init(std::string const &conf)
// Data for eABF z-based estimator
if (b_extended) {
get_keyval(conf, "CZARestimator", b_CZAR_estimator, true);
// CZAR output files for stratified eABF
get_keyval(conf, "writeCZARwindowFile", b_czar_window_file, false,
colvarparse::parse_silent);
@ -187,8 +190,38 @@ int colvarbias_abf::init(std::string const &conf)
read_gradients_samples();
}
cvm::log("Finished ABF setup.\n");
// if extendedLangrangian is on, then call UI estimator
if (b_extended) {
get_keyval(conf, "UIestimator", b_UI_estimator, false);
if (b_UI_estimator) {
std::vector<double> UI_lowerboundary;
std::vector<double> UI_upperboundary;
std::vector<double> UI_width;
std::vector<double> UI_krestr;
bool UI_restart = (input_prefix.size() > 0);
for (size_t i = 0; i < colvars.size(); i++)
{
UI_lowerboundary.push_back(colvars[i]->lower_boundary);
UI_upperboundary.push_back(colvars[i]->upper_boundary);
UI_width.push_back(colvars[i]->width);
UI_krestr.push_back(colvars[i]->force_constant());
}
eabf_UI = UIestimator::UIestimator(UI_lowerboundary,
UI_upperboundary,
UI_width,
UI_krestr, // force constant in eABF
output_prefix, // the prefix of output files
cvm::restart_out_freq,
UI_restart, // whether restart from a .count and a .grad file
input_prefix, // the prefixes of input files
cvm::temperature());
}
}
cvm::log("Finished ABF setup.\n");
return COLVARS_OK;
}
@ -332,7 +365,7 @@ int colvarbias_abf::update()
}
// update the output prefix; TODO: move later to setup_output() function
if (cvm::num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
if (cvm::main()->num_biases_feature(colvardeps::f_cvb_calc_pmf) == 1) {
// This is the only bias computing PMFs
output_prefix = cvm::output_prefix();
} else {
@ -364,6 +397,20 @@ int colvarbias_abf::update()
cvm::log("Prepared sample and gradient buffers at step "+cvm::to_str(cvm::step_absolute())+".");
}
// update UI estimator every step
if (b_UI_estimator)
{
std::vector<double> x(colvars.size(),0);
std::vector<double> y(colvars.size(),0);
for (size_t i = 0; i < colvars.size(); i++)
{
x[i] = colvars[i]->actual_value();
y[i] = colvars[i]->value();
}
eabf_UI.update_output_filename(output_prefix);
eabf_UI.update(cvm::step_absolute(), x, y);
}
return COLVARS_OK;
}
@ -479,8 +526,8 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool app
cvm::proxy->close_output_stream(pmf_out_name);
}
if (z_gradients) {
// Write eABF-related quantities
if (b_CZAR_estimator) {
// Write eABF CZAR-related quantities
std::string z_samples_out_name = prefix + ".zcount";
@ -588,7 +635,7 @@ void colvarbias_abf::read_gradients_samples()
is.close();
}
if (z_gradients) {
if (b_CZAR_estimator) {
// 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);
@ -621,7 +668,7 @@ std::ostream & colvarbias_abf::write_state_data(std::ostream& os)
os << "\ngradient\n";
gradients->write_raw(os, 8);
if (z_gradients) {
if (b_CZAR_estimator) {
os.setf(std::ios::fmtflags(0), std::ios::floatfield); // default floating-point format
os << "\nz_samples\n";
z_samples->write_raw(os, 8);
@ -655,7 +702,7 @@ std::istream & colvarbias_abf::read_state_data(std::istream& is)
return is;
}
if (z_gradients) {
if (b_CZAR_estimator) {
if (! read_state_data_key(is, "z_samples")) {
return is;