Update Colvars to version 2022-05-09

This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.

Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).

Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers.  Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.

The following pull requests in the Colvars repository are relevant to LAMMPS:

- 475 Remove fatal error condition
  https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)

- 474 Allow normalizing eigenvector vector components to deal with unit change
  https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)

- 470 Better error handling in the initialization of NeuralNetwork CV
  https://github.com/Colvars/colvars/pull/470 (@HanatoK)

- 468 Add examples of histogram configuration, with and without explicit grid parameters
  https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)

- 464 Fix #463 using more fine-grained features
  https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)

- 447 [RFC] New option "scaledBiasingForce" for colvarbias
  https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)

- 444 [RFC] Implementation of dense neural network as CV
  https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)

- 443 Fix explicit gradient dependency of sub-CVs
  https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)

- 442 Persistent bias count
  https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)

- 437 Return type of bias from scripting interface
  https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)

- 434 More flexible use of boundaries from colvars by grids
  https://github.com/Colvars/colvars/pull/434 (@jhenin)

- 433 Prevent double-free in linearCombination
  https://github.com/Colvars/colvars/pull/433 (@HanatoK)

- 428 More complete documentation for index file format (NDX)
  https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)

- 426 Integrate functional version of backup_file() into base proxy class
  https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)

- 424 Track CVC inheritance when documenting feature usage
  https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)

- 419 Generate citation report while running computations
  https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)

- 415 Rebin metadynamics bias from explicit hills when available
  https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)

- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
  https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)

Authors: @giacomofiorin, @HanatoK, @jhenin

src/COLVARS/colvarproxy_lammps.cpp

@@ -27,35 +27,6 @@
 
 #define HASH_FAIL  -1
 
-////////////////////////////////////////////////////////////////////////
-// local helper functions
-
-// safely move filename to filename.extension
-static int my_backup_file(const char *filename, const char *extension)
-{
-  struct stat sbuf;
-  if (stat(filename, &sbuf) == 0) {
-    if (!extension) extension = ".BAK";
-    char *backup = new char[strlen(filename)+strlen(extension)+1];
-    strcpy(backup, filename);
-    strcat(backup, extension);
-#if defined(_WIN32) && !defined(__CYGWIN__)
-    remove(backup);
-#endif
-    if (rename(filename,backup)) {
-      char *sys_err_msg = strerror(errno);
-      if (!sys_err_msg)  sys_err_msg = (char *) "(unknown error)";
-      fprintf(stderr,"Error renaming file %s to %s: %s\n",
-              filename, backup, sys_err_msg);
-      delete [] backup;
-      return COLVARS_ERROR;
-    }
-    delete [] backup;
-  }
-  return COLVARS_OK;
-}
-
-////////////////////////////////////////////////////////////////////////
 
 colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
                                        const char *inp_name,
@@ -75,10 +46,6 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
   t_target=temp;
   do_exit=false;
 
-  // User-scripted forces are not available in LAMMPS
-  force_script_defined = false;
-  have_scripts = false;
-
   // set input restart name and strip the extension, if present
   input_prefix_str = std::string(inp_name ? inp_name : "");
   if (input_prefix_str.rfind(".colvars.state") != std::string::npos)
@@ -130,6 +97,9 @@ void colvarproxy_lammps::init(const char *conf_file)
   cvm::log("Using LAMMPS interface, version "+
            cvm::to_str(COLVARPROXY_VERSION)+".\n");
 
+  colvars->cite_feature("LAMMPS engine");
+  colvars->cite_feature("Colvars-LAMMPS interface");
+
   my_angstrom  = _lmp->force->angstrom;
   // Front-end unit is the same as back-end
   angstrom_value = my_angstrom;
@@ -179,10 +149,6 @@ int colvarproxy_lammps::read_state_file(char const *state_filename)
 colvarproxy_lammps::~colvarproxy_lammps()
 {
   delete _random;
-  if (colvars != nullptr) {
-    delete colvars;
-    colvars = nullptr;
-  }
 }
 
 // re-initialize data where needed
@@ -339,17 +305,6 @@ int colvarproxy_lammps::set_unit_system(std::string const &units_in, bool /*chec
 }
 
 
-int colvarproxy_lammps::backup_file(char const *filename)
-{
-  if (std::string(filename).rfind(std::string(".colvars.state"))
-      != std::string::npos) {
-    return my_backup_file(filename, ".old");
-  } else {
-    return my_backup_file(filename, ".BAK");
-  }
-}
-
-
 // multi-replica support
 
 int colvarproxy_lammps::replica_enabled()
@@ -414,8 +369,8 @@ int colvarproxy_lammps::check_atom_id(int atom_number)
   // TODO add upper boundary check?
   if ((aid < 0)) {
     cvm::error("Error: invalid atom number specified, "+
-               cvm::to_str(atom_number)+"\n", INPUT_ERROR);
-    return INPUT_ERROR;
+               cvm::to_str(atom_number)+"\n", COLVARS_INPUT_ERROR);
+    return COLVARS_INPUT_ERROR;
   }
 
   return aid;

src/COLVARS/colvarproxy_lammps.h

@@ -101,10 +101,7 @@ class colvarproxy_lammps : public colvarproxy {
   void log(std::string const &message) override;
   void error(std::string const &message) override;
 
-  cvm::rvector position_distance(cvm::atom_pos const &pos1,
-                                 cvm::atom_pos const &pos2) const override;
-
-  int backup_file(char const *filename) override;
+  cvm::rvector position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const override;
 
   cvm::real rand_gaussian(void) override { return _random->gaussian(); };
 

src/COLVARS/colvarproxy_lammps_version.h

@@ -1,3 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2021-03-02"
+#define COLVARPROXY_VERSION "2022-05-09"
 #endif

src/COLVARS/fix_colvars.cpp

@@ -38,23 +38,14 @@
 #include "universe.h"
 #include "update.h"
 
-#include "colvarproxy_lammps.h"
-#include "colvarmodule.h"
-
 #include <cstring>
 #include <iostream>
 #include <memory>
+#include <vector>
+
+#include "colvarproxy_lammps.h"
+#include "colvarmodule.h"
 
-static const char colvars_pub[] =
-  "fix colvars command:\n\n"
-  "@Article{fiorin13,\n"
-  " author =  {G.~Fiorin and M.{\\,}L.~Klein and J.~H{\\'e}nin},\n"
-  " title =   {Using collective variables to drive molecular"
-  " dynamics simulations},\n"
-  " journal = {Mol.~Phys.},\n"
-  " year =    2013,\n"
-  " note =    {doi: 10.1080/00268976.2013.813594}\n"
-  "}\n\n";
 
 /* struct for packed data communication of coordinates and forces. */
 struct LAMMPS_NS::commdata {
@@ -349,8 +340,6 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
 
   /* storage required to communicate a single coordinate or force. */
   size_one = sizeof(struct commdata);
-
-  if (lmp->citeme) lmp->citeme->add(colvars_pub);
 }
 
 /*********************************
@@ -978,6 +967,9 @@ void FixColvars::post_run()
 {
   if (me == 0) {
     proxy->post_run();
+    if (lmp->citeme) {
+      lmp->citeme->add(proxy->colvars->feature_report(1));
+    }
   }
 }