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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

32
lib/colvars/colvar_neuralnetworkcompute.cpp
View File

@ -1,6 +1,19 @@
// -*- Mode:c++; c-basic-offset: 4; -*-
// This file is part of the Collective Variables module (Colvars).
// The original version of Colvars and its updates are located at:
// https://github.com/Colvars/colvars
// Please update all Colvars source files before making any changes.
// If you wish to distribute your changes, please submit them to the
// Colvars repository at GitHub.
#include <iostream>
#include <fstream>
#if (__cplusplus >= 201103L)
#include "colvar_neuralnetworkcompute.h"
#include "colvarparse.h"
#include "colvarproxy.h"
namespace neuralnetworkCV {
std::map<std::string, std::pair<std::function<double(double)>, std::function<double(double)>>> activation_function_map
@ -124,12 +137,10 @@ void denseLayer::readFromFile(const std::string& weights_file, const std::string
m_weights.clear();
m_biases.clear();
std::string line;
std::ifstream ifs_weights(weights_file.c_str());
if (!ifs_weights) {
throw std::runtime_error("Cannot open file " + weights_file);
}
colvarproxy *proxy = cvm::main()->proxy;
auto &ifs_weights = proxy->input_stream(weights_file, "weights file");
while (std::getline(ifs_weights, line)) {
if (ifs_weights.bad()) {
if (!ifs_weights) {
throw std::runtime_error("I/O error while reading " + weights_file);
}
std::vector<std::string> splitted_data;
@ -146,13 +157,12 @@ void denseLayer::readFromFile(const std::string& weights_file, const std::string
m_weights.push_back(weights_tmp);
}
}
proxy->close_input_stream(weights_file);
// parse biases file
std::ifstream ifs_biases(biases_file.c_str());
if (!ifs_biases) {
throw std::runtime_error("Cannot open file " + biases_file);
}
auto &ifs_biases = proxy->input_stream(biases_file, "biases file");
while (std::getline(ifs_biases, line)) {
if (ifs_biases.bad()) {
if (!ifs_biases) {
throw std::runtime_error("I/O error while reading " + biases_file);
}
std::vector<std::string> splitted_data;
@ -167,6 +177,8 @@ void denseLayer::readFromFile(const std::string& weights_file, const std::string
m_biases.push_back(bias);
}
}
proxy->close_input_stream(biases_file);
m_input_size = m_weights[0].size();
m_output_size = m_weights.size();
}