Update Colvars library to version 2023-05-01

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

lib/colvars/colvarcomp_protein.cpp

@@ -86,7 +86,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
   {
     cvm::real r0;
     size_t en, ed;
-    get_keyval(conf, "hBondCutoff",   r0, (3.3 * proxy->angstrom_value));
+    get_keyval(conf, "hBondCutoff",   r0, proxy->angstrom_to_internal(3.3));
     get_keyval(conf, "hBondExpNumer", en, 6);
     get_keyval(conf, "hBondExpDenom", ed, 8);
 
@@ -333,10 +333,11 @@ colvar::dihedPC::dihedPC(std::string const &conf)
       return;
     }
 
-    std::ifstream vecFile;
-    vecFile.open(vecFileName.c_str());
-    if (!vecFile.good()) {
-      cvm::error("Error opening dihedral PCA vector file " + vecFileName + " for reading");
+    std::istream &vecFile =
+      cvm::main()->proxy->input_stream(vecFileName,
+                                       "dihedral PCA vector file");
+    if (!vecFile) {
+      return;
     }
 
     // TODO: adapt to different formats by setting this flag
@@ -375,7 +376,7 @@ colvar::dihedPC::dihedPC(std::string const &conf)
       }
     }
  */
-    vecFile.close();
+    cvm::main()->proxy->close_input_stream(vecFileName);
 
   } else {
     get_keyval(conf, "vector", coeffs, coeffs);