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Update Colvars library to version 2023-05-01

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This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
This commit is contained in:
Giacomo Fiorin
2023-05-17 13:29:00 -04:00
parent 166301180b
commit 377c652a83
53 changed files with 2575 additions and 2273 deletions
Download Patch File Download Diff File Expand all files Collapse all files

77
lib/colvars/colvarbias_abf.cpp
View File

@ -7,6 +7,8 @@
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <iostream>
#include "colvarmodule.h"
#include "colvar.h"
#include "colvarbias_abf.h"
@ -38,17 +40,17 @@ colvarbias_abf::colvarbias_abf(char const *key)
int colvarbias_abf::init(std::string const &conf)
{
colvarproxy *proxy = cvm::main()->proxy;
colvarbias::init(conf);
cvm::main()->cite_feature("ABF colvar bias implementation");
colvarproxy *proxy = cvm::main()->proxy;
enable(f_cvb_scalar_variables);
enable(f_cvb_calc_pmf);
// TODO relax this in case of VMD plugin
if (cvm::temperature() == 0.0)
if ((proxy->target_temperature() == 0.0) && proxy->simulation_running()) {
cvm::log("WARNING: ABF should not be run without a thermostat or at 0 Kelvin!\n");
}
// ************* parsing general ABF options ***********************
@ -277,7 +279,7 @@ int colvarbias_abf::init(std::string const &conf)
cvm::restart_out_freq,
UI_restart, // whether restart from a .count and a .grad file
input_prefix, // the prefixes of input files
cvm::temperature());
proxy->target_temperature());
}
}
@ -599,17 +601,17 @@ int colvarbias_abf::replica_share() {
template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
std::string const &filename,
bool close) {
std::ostream *os = cvm::proxy->output_stream(filename);
std::ostream &os = cvm::proxy->output_stream(filename);
if (!os) {
return cvm::error("Error opening file " + filename + " for writing.\n", COLVARS_ERROR | COLVARS_FILE_ERROR);
}
grid->write_multicol(*os);
grid->write_multicol(os);
if (close) {
cvm::proxy->close_output_stream(filename);
} else {
// Insert empty line between frames in history files
*os << std::endl;
cvm::proxy->flush_output_stream(os);
os << std::endl;
cvm::proxy->flush_output_stream(filename);
}
// In dimension higher than 2, dx is easier to handle and visualize
@ -617,11 +619,11 @@ template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
// (could be implemented as multiple dx files)
if (num_variables() > 2 && close) {
std::string dx = filename + ".dx";
std::ostream *dx_os = cvm::proxy->output_stream(dx);
std::ostream &dx_os = cvm::proxy->output_stream(dx);
if (!dx_os) {
return cvm::error("Error opening file " + dx + " for writing.\n", COLVARS_ERROR | COLVARS_FILE_ERROR);
}
grid->write_opendx(*dx_os);
grid->write_opendx(dx_os);
// if (close) {
cvm::proxy->close_output_stream(dx);
// }
@ -637,6 +639,8 @@ template <class T> int colvarbias_abf::write_grid_to_file(T const *grid,
void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool close)
{
colvarproxy *proxy = cvm::main()->proxy;
write_grid_to_file<colvar_grid_count>(samples, prefix + ".count", close);
write_grid_to_file<colvar_grid_gradient>(gradients, prefix + ".grad", close);
@ -660,7 +664,7 @@ void colvarbias_abf::write_gradients_samples(const std::string &prefix, bool clo
czar_gradients->index_ok(ix); czar_gradients->incr(ix)) {
for (size_t n = 0; n < czar_gradients->multiplicity(); n++) {
czar_gradients->set_value(ix, z_gradients->value_output(ix, n)
- cvm::temperature() * cvm::boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
- proxy->target_temperature() * proxy->boltzmann() * z_samples->log_gradient_finite_diff(ix, n), n);
}
}
write_grid_to_file<colvar_grid_gradient>(czar_gradients, prefix + ".czar.grad", close);
@ -698,8 +702,10 @@ int colvarbias_abf::bin_count(int bin_index) {
}
void colvarbias_abf::read_gradients_samples()
int colvarbias_abf::read_gradients_samples()
{
int error_code = COLVARS_OK;
std::string samples_in_name, gradients_in_name, z_samples_in_name, z_gradients_in_name;
for ( size_t i = 0; i < input_prefix.size(); i++ ) {
@ -708,43 +714,30 @@ void colvarbias_abf::read_gradients_samples()
z_samples_in_name = input_prefix[i] + ".zcount";
z_gradients_in_name = input_prefix[i] + ".zgrad";
// For user-provided files, the per-bias naming scheme may not apply
cvm::log("Reading sample count from " + samples_in_name +
" and gradient from " + gradients_in_name);
std::ifstream is;
error_code |= samples->read_multicol(samples_in_name,
"ABF samples file",
true);
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);
is.close();
is.clear();
is.open(gradients_in_name.c_str());
if (!is.is_open()) {
cvm::error("Error opening ABF gradient file " +
gradients_in_name + " for reading", COLVARS_INPUT_ERROR);
} else {
gradients->read_multicol(is, true);
is.close();
}
error_code |= gradients->read_multicol(gradients_in_name,
"ABF gradient file",
true);
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);
is.clear();
is.open(z_samples_in_name.c_str());
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 eABF z-gradient file " + z_gradients_in_name + " for reading");
z_gradients->read_multicol(is, true);
is.close();
error_code |= z_samples->read_multicol(z_samples_in_name,
"eABF z-histogram file",
true);
error_code |= z_gradients->read_multicol(z_gradients_in_name,
"eABF z-gradient file",
true);
}
}
return;
return error_code;
}