Update Colvars library to version 2020-01-27

One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279

lib/colvars/Makefile.common

@@ -31,6 +31,7 @@ COLVARS_SRCS = \
         colvarbias_meta.cpp \
         colvarbias_restraint.cpp \
         colvarcomp_angles.cpp \
+        colvarcomp_apath.cpp \
         colvarcomp_coordnums.cpp \
         colvarcomp.cpp \
         colvarcomp_distances.cpp \
@@ -41,8 +42,10 @@ COLVARS_SRCS = \
         colvardeps.cpp \
         colvargrid.cpp \
         colvarmodule.cpp \
+        colvarparams.cpp \
         colvarparse.cpp \
         colvarproxy.cpp \
+        colvarproxy_replicas.cpp \
         colvarscript.cpp \
         colvartypes.cpp \
         colvarvalue.cpp

lib/colvars/Makefile.deps

@@ -1,235 +1,90 @@
 
 $(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
- colvarparse.h colvaratoms.h colvardeps.h
+ colvarparse.h colvarparams.h colvaratoms.h colvardeps.h
 $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
- colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvardeps.h colvarbias_abf.h colvarbias.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvargrid.h colvar_UIestimator.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarbias_abf.h colvarbias.h colvargrid.h colvar_UIestimator.h
 $(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \
  colvars_version.h colvarbias.h colvar.h colvarvalue.h colvartypes.h \
- colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvardeps.h colvarbias_alb.h
- lepton/include/lepton/CompiledExpression.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarbias_alb.h
 $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvarbias.h \
- colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ colvar.h colvarparse.h colvarparams.h colvardeps.h colvargrid.h
- lepton/include/lepton/CompiledExpression.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \
  colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
- colvarvalue.h colvar.h colvarparse.h colvardeps.h \
+ colvarvalue.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
- lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
  colvarbias_histogram.h colvarbias.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvar.h \
- colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvardeps.h colvarbias_meta.h colvarbias.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvargrid.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarbias_meta.h colvarbias.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \
  colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
  colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \
- colvardeps.h lepton/include/Lepton.h \
+ colvarparams.h colvardeps.h
- lepton/include/lepton/CompiledExpression.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h
 $(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \
  colvarmodule.h colvars_version.h colvar.h colvarvalue.h colvartypes.h \
- colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvarproxy.h colvar_arithmeticpath.h
- lepton/include/lepton/ExpressionTreeNode.h \
+$(COLVARS_OBJ_DIR)colvarcomp_apath.o: colvarcomp_apath.cpp
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h
 $(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \
  colvarmodule.h colvars_version.h colvarparse.h colvarvalue.h \
- colvartypes.h colvaratoms.h colvarproxy.h colvardeps.h colvar.h \
+ colvartypes.h colvarparams.h colvaratoms.h colvarproxy.h colvardeps.h \
- lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ colvar.h colvarcomp.h colvar_arithmeticpath.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h
 $(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h colvar.h colvarparse.h \
- colvardeps.h lepton/include/Lepton.h \
+ colvarparams.h colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvar_arithmeticpath.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h
 $(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
- lepton/include/lepton/ExpressionTreeNode.h \
+$(COLVARS_OBJ_DIR)colvarcomp_gpath.o: colvarcomp_gpath.cpp
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h
 $(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h
 $(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarparse.h colvar.h colvardeps.h lepton/include/Lepton.h \
+ colvarparse.h colvarparams.h colvar.h colvardeps.h colvarcomp.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvaratoms.h colvarproxy.h colvar_arithmeticpath.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h
 $(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \
- colvarvalue.h colvartypes.h colvarparse.h colvar.h colvardeps.h \
+ colvarvalue.h colvartypes.h colvarparse.h colvarparams.h colvar.h \
- lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ colvardeps.h colvarcomp.h colvaratoms.h colvarproxy.h \
- lepton/include/lepton/ExpressionTreeNode.h \
+ colvar_arithmeticpath.h colvarscript.h colvarbias.h
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h colvarscript.h colvarbias.h
 $(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h colvardeps.h \
- colvarparse.h
+ colvarparse.h colvarparams.h
 $(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \
- colvars_version.h colvarvalue.h colvartypes.h colvarparse.h colvar.h \
+ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
- colvardeps.h lepton/include/Lepton.h \
+ colvarparams.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvarproxy.h colvar_arithmeticpath.h colvargrid.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarcomp.h colvaratoms.h colvarproxy.h colvargrid.h
 $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \
  colvars_version.h colvarparse.h colvarvalue.h colvartypes.h \
- colvarproxy.h colvar.h colvardeps.h lepton/include/Lepton.h \
+ colvarparams.h colvarproxy.h colvar.h colvardeps.h colvarbias.h \
- lepton/include/lepton/CompiledExpression.h \
+ colvarbias_abf.h colvargrid.h colvar_UIestimator.h colvarbias_alb.h \
- lepton/include/lepton/ExpressionTreeNode.h \
+ colvarbias_histogram.h colvarbias_meta.h colvarbias_restraint.h \
- lepton/include/lepton/windowsIncludes.h \
+ colvarscript.h colvaratoms.h colvarcomp.h colvar_arithmeticpath.h
- lepton/include/lepton/CustomFunction.h \
+$(COLVARS_OBJ_DIR)colvarparams.o: colvarparams.cpp colvarmodule.h \
- lepton/include/lepton/ExpressionProgram.h \
+ colvars_version.h colvarvalue.h colvartypes.h colvarparams.h
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \
- colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \
- colvarbias_restraint.h colvarscript.h colvaratoms.h colvarcomp.h
 $(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \
- colvars_version.h colvarvalue.h colvartypes.h colvarparse.h
+ colvars_version.h colvarvalue.h colvartypes.h colvarparse.h \
+ colvarparams.h
 $(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \
  colvars_version.h colvarproxy.h colvartypes.h colvarvalue.h \
- colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \
+ colvarscript.h colvarbias.h colvar.h colvarparse.h colvarparams.h \
- lepton/include/Lepton.h lepton/include/lepton/CompiledExpression.h \
+ colvardeps.h colvaratoms.h
- lepton/include/lepton/ExpressionTreeNode.h \
+$(COLVARS_OBJ_DIR)colvarproxy_replicas.o: colvarproxy_replicas.cpp \
- lepton/include/lepton/windowsIncludes.h \
+ colvarmodule.h colvars_version.h colvarproxy.h colvartypes.h \
- lepton/include/lepton/CustomFunction.h \
+ colvarvalue.h
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
- colvaratoms.h
 $(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \
  colvarmodule.h colvars_version.h colvarvalue.h colvartypes.h \
- colvarbias.h colvar.h colvarparse.h colvardeps.h lepton/include/Lepton.h \
+ colvarbias.h colvar.h colvarparse.h colvarparams.h colvardeps.h \
- lepton/include/lepton/CompiledExpression.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/windowsIncludes.h \
- lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/ExpressionProgram.h \
- lepton/include/lepton/ExpressionTreeNode.h \
- lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \
- lepton/include/lepton/Exception.h \
- lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \
  colvarproxy.h
 $(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \
- colvars_version.h colvartypes.h colvarparse.h colvarvalue.h
+ colvars_version.h colvartypes.h colvarparse.h colvarvalue.h \
+ colvarparams.h
 $(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \
  colvars_version.h colvarvalue.h colvartypes.h

lib/colvars/colvar.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -29,6 +29,10 @@ colvar::colvar()
   kinetic_energy = 0.0;
   potential_energy = 0.0;
 
+#ifdef LEPTON
+  dev_null = 0.0;
+#endif
+
   description = "uninitialized colvar";
   init_dependencies();
 }
@@ -194,23 +198,32 @@ int colvar::init(std::string const &conf)
   {
     bool homogeneous = is_enabled(f_cv_linear);
     for (i = 0; i < cvcs.size(); i++) {
-      if ((cvm::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) {
+      if (cvm::fabs(cvm::fabs(cvcs[i]->sup_coeff) - 1.0) > 1.0e-10) {
         homogeneous = false;
       }
     }
     set_enabled(f_cv_homogeneous, homogeneous);
   }
 
+  // A single-component variable almost concides with its CVC object
+  if ((cvcs.size() == 1) && is_enabled(f_cv_homogeneous)) {
+    if ( !is_enabled(f_cv_scripted) && !is_enabled(f_cv_custom_function) &&
+         (cvm::fabs(cvcs[0]->sup_coeff - 1.0) < 1.0e-10) &&
+         (cvcs[0]->sup_np == 1) ) {
+      enable(f_cv_single_cvc);
+    }
+  }
+
   // Colvar is deemed periodic if:
   // - it is homogeneous
   // - all cvcs are periodic
   // - all cvcs have the same period
-  if (is_enabled(f_cv_homogeneous) && cvcs[0]->b_periodic) { // TODO make this a CVC feature
+  if (is_enabled(f_cv_homogeneous) && cvcs[0]->is_enabled(f_cvc_periodic)) {
     bool b_periodic = true;
     period = cvcs[0]->period;
     wrap_center = cvcs[0]->wrap_center;
     for (i = 1; i < cvcs.size(); i++) {
-      if (!cvcs[i]->b_periodic || cvcs[i]->period != period) {
+      if (!cvcs[i]->is_enabled(f_cvc_periodic) || cvcs[i]->period != period) {
         b_periodic = false;
         period = 0.0;
         cvm::log("Warning: although one component is periodic, this colvar will "
@@ -296,13 +309,13 @@ int colvar::init(std::string const &conf)
 #ifdef LEPTON
 int colvar::init_custom_function(std::string const &conf)
 {
-  std::string expr;
+  std::string expr, expr_in; // expr_in is a buffer to remember expr after unsuccessful parsing
   std::vector<Lepton::ParsedExpression> pexprs;
   Lepton::ParsedExpression pexpr;
   size_t pos = 0; // current position in config string
   double *ref;
 
-  if (!key_lookup(conf, "customFunction", &expr, &pos)) {
+  if (!key_lookup(conf, "customFunction", &expr_in, &pos)) {
     return COLVARS_OK;
   }
 
@@ -310,6 +323,7 @@ int colvar::init_custom_function(std::string const &conf)
   cvm::log("This colvar uses a custom function.\n");
 
   do {
+    expr = expr_in;
     if (cvm::debug())
       cvm::log("Parsing expression \"" + expr + "\".\n");
     try {
@@ -337,8 +351,7 @@ int colvar::init_custom_function(std::string const &conf)
             // To keep the same workflow, we use a pointer to a double here
             // that will receive CVC values - even though none was allocated by Lepton
             ref = &dev_null;
-            if (cvm::debug())
+            cvm::log("Warning: Variable " + vn + " is absent from expression \"" + expr + "\".\n");
-              cvm::log("Variable " + vn + " is absent from expression \"" + expr + "\".\n");
           }
           value_eval_var_refs.push_back(ref);
         }
@@ -348,7 +361,7 @@ int colvar::init_custom_function(std::string const &conf)
       cvm::error("Error compiling expression \"" + expr + "\".\n", INPUT_ERROR);
       return INPUT_ERROR;
     }
-  } while (key_lookup(conf, "customFunction", &expr, &pos));
+  } while (key_lookup(conf, "customFunction", &expr_in, &pos));
 
 
   // Now define derivative with respect to each scalar sub-component
@@ -373,8 +386,7 @@ int colvar::init_custom_function(std::string const &conf)
             catch (...) { // Variable is absent from derivative
               // To keep the same workflow, we use a pointer to a double here
               // that will receive CVC values - even though none was allocated by Lepton
-              if (cvm::debug())
+              cvm::log("Warning: Variable " + vvn + " is absent from derivative of \"" + expr + "\" wrt " + vn + ".\n");
-                cvm::log("Variable " + vvn + " is absent from derivative of \"" + expr + "\" wrt " + vn + ".\n");
               ref = &dev_null;
             }
             grad_eval_var_refs.push_back(ref);
@@ -439,6 +451,21 @@ int colvar::init_custom_function(std::string const &conf)
 
 int colvar::init_custom_function(std::string const &conf)
 {
+
+  std::string expr;
+  size_t pos = 0;
+  if (key_lookup(conf, "customFunction", &expr, &pos)) {
+    std::string msg("Error: customFunction requires the Lepton library.");
+#if (__cplusplus < 201103L)
+    // NOTE: this is not ideal; testing for the Lepton library's version would
+    // be more accurate, but also less portable
+    msg +=
+      std::string("  Note also that recent versions of Lepton require C++11: "
+                  "please see https://colvars.github.io/README-c++11.html.");
+#endif
+    return cvm::error(msg, COLVARS_NOT_IMPLEMENTED);
+  }
+
   return COLVARS_OK;
 }
 
@@ -449,7 +476,19 @@ int colvar::init_grid_parameters(std::string const &conf)
 {
   colvarmodule *cv = cvm::main();
 
-  get_keyval(conf, "width", width, 1.0);
+  cvm::real default_width = width;
+
+  if (!key_already_set("width")) {
+    // The first time, check if the CVC has a width to provide
+    default_width = 1.0;
+    if (is_enabled(f_cv_single_cvc) && cvcs[0]->is_enabled(f_cvc_width)) {
+      cvm::real const cvc_width = cvcs[0]->get_param("width");
+      default_width = cvc_width;
+    }
+  }
+
+  get_keyval(conf, "width", width, default_width);
+
   if (width <= 0.0) {
     cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
     return INPUT_ERROR;
@@ -460,12 +499,32 @@ int colvar::init_grid_parameters(std::string const &conf)
 
   if (is_enabled(f_cv_scalar)) {
 
+    if (is_enabled(f_cv_single_cvc)) {
+      // Get the default boundaries from the component
+      if (cvcs[0]->is_enabled(f_cvc_lower_boundary)) {
+        enable(f_cv_lower_boundary);
+        enable(f_cv_hard_lower_boundary);
+        lower_boundary =
+          *(reinterpret_cast<colvarvalue const *>(cvcs[0]->get_param_ptr("lowerBoundary")));
+      }
+      if (cvcs[0]->is_enabled(f_cvc_upper_boundary)) {
+        enable(f_cv_upper_boundary);
+        enable(f_cv_hard_upper_boundary);
+        upper_boundary =
+          *(reinterpret_cast<colvarvalue const *>(cvcs[0]->get_param_ptr("upperBoundary")));
+      }
+    }
+
     if (get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary)) {
       enable(f_cv_lower_boundary);
+      // Because this is the user's choice, we cannot assume it is a true
+      // physical boundary
+      disable(f_cv_hard_lower_boundary);
     }
 
     if (get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary)) {
       enable(f_cv_upper_boundary);
+      disable(f_cv_hard_upper_boundary);
     }
 
     std::string lw_conf, uw_conf;
@@ -520,12 +579,11 @@ harmonicWalls {\n\
     }
   }
 
-  if (is_enabled(f_cv_lower_boundary)) {
+  get_keyval_feature(this, conf, "hardLowerBoundary", f_cv_hard_lower_boundary,
-    get_keyval(conf, "hardLowerBoundary", hard_lower_boundary, false);
+                     is_enabled(f_cv_hard_lower_boundary));
-  }
+
-  if (is_enabled(f_cv_upper_boundary)) {
+  get_keyval_feature(this, conf, "hardUpperBoundary", f_cv_hard_upper_boundary,
-    get_keyval(conf, "hardUpperBoundary", hard_upper_boundary, false);
+                     is_enabled(f_cv_hard_upper_boundary));
-  }
 
   // consistency checks for boundaries and walls
   if (is_enabled(f_cv_lower_boundary) && is_enabled(f_cv_upper_boundary)) {
@@ -546,7 +604,8 @@ harmonicWalls {\n\
                INPUT_ERROR);
     return INPUT_ERROR;
   }
-  if (expand_boundaries && hard_lower_boundary && hard_upper_boundary) {
+  if (expand_boundaries && is_enabled(f_cv_hard_lower_boundary) &&
+      is_enabled(f_cv_hard_upper_boundary)) {
     cvm::error("Error: inconsistent configuration "
                "(trying to expand boundaries with both "
                "hardLowerBoundary and hardUpperBoundary enabled).\n",
@@ -568,7 +627,8 @@ int colvar::init_extended_Lagrangian(std::string const &conf)
     cvm::log("Enabling the extended Lagrangian term for colvar \""+
              this->name+"\".\n");
 
-    x_ext.type(value());
+    // Mark x_ext as uninitialized so we can initialize it to the colvar value when updating
+    x_ext.type(colvarvalue::type_notset);
     v_ext.type(value());
     fr.type(value());
 
@@ -646,7 +706,7 @@ int colvar::init_output_flags(std::string const &conf)
     bool temp;
     if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) {
       cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n"
-                 "The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
+                 "The two are NOT identical: see https://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
       return INPUT_ERROR;
     }
   }
@@ -664,7 +724,7 @@ int colvar::init_output_flags(std::string const &conf)
 // read the configuration and set up corresponding instances, for
 // each type of component implemented
 template<typename def_class_name> int colvar::init_components_type(std::string const &conf,
-                                                                   char const *def_desc,
+                                                                   char const * /* def_desc */,
                                                                    char const *def_config_key)
 {
   size_t def_count = 0;
@@ -744,6 +804,7 @@ template<typename def_class_name> int colvar::init_components_type(std::string c
 int colvar::init_components(std::string const &conf)
 {
   int error_code = COLVARS_OK;
+  size_t i = 0, j = 0;
 
   error_code |= init_components_type<distance>(conf, "distance", "distance");
   error_code |= init_components_type<distance_vec>(conf, "distance vector", "distanceVec");
@@ -793,9 +854,11 @@ int colvar::init_components(std::string const &conf)
   error_code |= init_components_type<eigenvector>(conf, "eigenvector", "eigenvector");
   error_code |= init_components_type<gspath>(conf, "geometrical path collective variables (s)", "gspath");
   error_code |= init_components_type<gzpath>(conf, "geometrical path collective variables (z)", "gzpath");
-  error_code |= init_components_type<linearCombination>(conf, "linear combination of other collective variables", "subColvar");
+  error_code |= init_components_type<linearCombination>(conf, "linear combination of other collective variables", "linearCombination");
   error_code |= init_components_type<gspathCV>(conf, "geometrical path collective variables (s) for other CVs", "gspathCV");
   error_code |= init_components_type<gzpathCV>(conf, "geometrical path collective variables (z) for other CVs", "gzpathCV");
+  error_code |= init_components_type<aspathCV>(conf, "arithmetic path collective variables (s) for other CVs", "aspathCV");
+  error_code |= init_components_type<azpathCV>(conf, "arithmetic path collective variables (s) for other CVs", "azpathCV");
 
   if (!cvcs.size() || (error_code != COLVARS_OK)) {
     cvm::error("Error: no valid components were provided "
@@ -804,15 +867,26 @@ int colvar::init_components(std::string const &conf)
     return INPUT_ERROR;
   }
 
+  // Check for uniqueness of CVC names (esp. if user-provided)
+  for (i = 0; i < cvcs.size(); i++) {
+    for (j = i+1; j < cvcs.size(); j++) {
+      if (cvcs[i]->name == cvcs[j]->name) {
+        cvm::error("Components " + cvm::to_str(i) + " and " + cvm::to_str(j) +\
+          " cannot have the same name \"" +  cvcs[i]->name+ "\".\n", INPUT_ERROR);
+        return INPUT_ERROR;
+      }
+    }
+  }
+
   n_active_cvcs = cvcs.size();
 
-  cvm::log("All components initialized.\n");
-
   // Store list of children cvcs for dependency checking purposes
-  for (size_t i = 0; i < cvcs.size(); i++) {
+  for (i = 0; i < cvcs.size(); i++) {
     add_child(cvcs[i]);
   }
 
+  cvm::log("All components initialized.\n");
+
   return COLVARS_OK;
 }
 
@@ -921,7 +995,7 @@ int colvar::parse_analysis(std::string const &conf)
         return cvm::error("Error: collective variable \""+acf_colvar_name+
                           "\" is not defined at this time.\n", INPUT_ERROR);
       }
-      cv2->enable(f_cv_fdiff_velocity);
+      cv2->enable(f_cv_fdiff_velocity); // Manual dependency to object of same type
     } else if (acf_type_str == to_lower_cppstr(std::string("coordinate_p2"))) {
       acf_type = acf_p2coor;
     } else {
@@ -998,6 +1072,8 @@ int colvar::init_dependencies() {
     init_feature(f_cv_Langevin, "Langevin dynamics", f_type_user);
     require_feature_self(f_cv_Langevin, f_cv_extended_Lagrangian);
 
+    init_feature(f_cv_single_cvc, "single component", f_type_static);
+
     init_feature(f_cv_linear, "linear", f_type_static);
 
     init_feature(f_cv_scalar, "scalar", f_type_static);
@@ -1023,6 +1099,12 @@ int colvar::init_dependencies() {
     init_feature(f_cv_upper_boundary, "upper boundary", f_type_user);
     require_feature_self(f_cv_upper_boundary, f_cv_scalar);
 
+    init_feature(f_cv_hard_lower_boundary, "hard lower boundary", f_type_user);
+    require_feature_self(f_cv_hard_lower_boundary, f_cv_lower_boundary);
+
+    init_feature(f_cv_hard_upper_boundary, "hard upper boundary", f_type_user);
+    require_feature_self(f_cv_hard_upper_boundary, f_cv_upper_boundary);
+
     init_feature(f_cv_grid, "grid", f_type_dynamic);
     require_feature_self(f_cv_grid, f_cv_lower_boundary);
     require_feature_self(f_cv_grid, f_cv_upper_boundary);
@@ -1227,7 +1309,7 @@ int colvar::collect_cvc_data()
 }
 
 
-int colvar::check_cvc_range(int first_cvc, size_t num_cvcs)
+int colvar::check_cvc_range(int first_cvc, size_t /* num_cvcs */)
 {
   if ((first_cvc < 0) || (first_cvc >= ((int) cvcs.size()))) {
     cvm::error("Error: trying to address a component outside the "
@@ -1512,7 +1594,7 @@ int colvar::calc_colvar_properties()
 
     // initialize the restraint center in the first step to the value
     // just calculated from the cvcs
-    if (cvm::step_relative() == 0 && !after_restart) {
+    if ((cvm::step_relative() == 0 && !after_restart) || x_ext.type() == colvarvalue::type_notset) {
       x_ext = x;
       v_ext.reset(); // (already 0; added for clarity)
     }
@@ -1859,6 +1941,59 @@ int colvar::update_cvc_config(std::vector<std::string> const &confs)
 }
 
 
+int colvar::cvc_param_exists(std::string const &param_name)
+{
+  if (is_enabled(f_cv_single_cvc)) {
+    return cvcs[0]->param_exists(param_name);
+  }
+  return cvm::error("Error: calling colvar::cvc_param_exists() for a variable "
+                    "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);
+}
+
+
+cvm::real colvar::get_cvc_param(std::string const &param_name)
+{
+  if (is_enabled(f_cv_single_cvc)) {
+    return cvcs[0]->get_param(param_name);
+  }
+  cvm::error("Error: calling colvar::get_cvc_param() for a variable "
+             "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);
+  return 0.0;
+}
+
+
+void const *colvar::get_cvc_param_ptr(std::string const &param_name)
+{
+  if (is_enabled(f_cv_single_cvc)) {
+    return cvcs[0]->get_param_ptr(param_name);
+  }
+  cvm::error("Error: calling colvar::get_cvc_param() for a variable "
+             "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);
+  return NULL;
+}
+
+
+colvarvalue const *colvar::get_cvc_param_grad(std::string const &param_name)
+{
+  if (is_enabled(f_cv_single_cvc)) {
+    return cvcs[0]->get_param_grad(param_name);
+  }
+  cvm::error("Error: calling colvar::get_cvc_param_grad() for a variable "
+             "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);
+  return NULL;
+}
+
+
+int colvar::set_cvc_param(std::string const &param_name, void const *new_value)
+{
+  if (is_enabled(f_cv_single_cvc)) {
+    return cvcs[0]->set_param(param_name, new_value);
+  }
+  return cvm::error("Error: calling colvar::set_cvc_param() for a variable "
+                    "with more than one component.\n", COLVARS_NOT_IMPLEMENTED);
+}
+
+
 // ******************** METRIC FUNCTIONS ********************
 // Use the metrics defined by \link colvar::cvc \endlink objects
 

lib/colvars/colvar.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -217,11 +217,11 @@ public:
   /// should equal the system force plus \link f \endlink
   colvarvalue ft;
 
-
   /// Period, if this variable is periodic
   cvm::real period;
-  cvm::real wrap_center;
 
+  /// Center of wrapping, if this variable is periodic
+  cvm::real wrap_center;
 
   /// \brief Expand the boundaries of multiples of width, to keep the
   /// value always within range
@@ -233,8 +233,6 @@ public:
   colvarvalue lower_wall;
   /// \brief Force constant for the lower boundary potential (|x-xb|^2)
   cvm::real   lower_wall_k;
-  /// \brief Whether this colvar has a hard lower boundary
-  bool        hard_lower_boundary;
 
   /// \brief Location of the upper boundary
   colvarvalue upper_boundary;
@@ -242,8 +240,6 @@ public:
   colvarvalue upper_wall;
   /// \brief Force constant for the upper boundary potential (|x-xb|^2)
   cvm::real   upper_wall_k;
-  /// \brief Whether this colvar has a hard upper boundary
-  bool        hard_upper_boundary;
 
   /// \brief Is the interval defined by the two boundaries periodic?
   bool periodic_boundaries() const;
@@ -356,7 +352,7 @@ public:
   /// colvar::update()) to the external degrees of freedom
   void communicate_forces();
 
-  /// \brief Enables and disables individual CVCs based on flags
+  /// \brief Enables and disables individual CVCs based on the given array
   int set_cvc_flags(std::vector<bool> const &flags);
 
   /// \brief Updates the flags in the CVC objects, and their number
@@ -365,7 +361,23 @@ public:
   /// \brief Modify the configuration of CVCs (currently, only base class data)
   int update_cvc_config(std::vector<std::string> const &confs);
 
+  /// Whether this named parameter exists (in the first and only component)
+  int cvc_param_exists(std::string const &param_name);
+
+  /// Get the value of the named parameter (from the first and only component)
+  cvm::real get_cvc_param(std::string const &param_name);
+
+  /// Get a pointer to the named parameter (from the first and only component)
+  void const *get_cvc_param_ptr(std::string const &param_name);
+
+  /// Pointer to the derivative of the variable with respect to param_name
+  colvarvalue const *get_cvc_param_grad(std::string const &param_name);
+
+  /// Set the named parameter in the first and only component to the given value
+  int set_cvc_param(std::string const &param_name, void const *new_value);
+
 protected:
+
   /// \brief Number of CVC objects with an active flag
   size_t n_active_cvcs;
 
@@ -380,11 +392,24 @@ protected:
 
 public:
 
-  /// \brief Return the number of CVC objects defined
+  /// \brief Number of dimensions of the value of this colvar
-  inline size_t num_cvcs() const { return cvcs.size(); }
+  inline size_t num_dimensions() const
+  {
+    return value().size();
+  }
 
-  /// \brief Return the number of CVC objects with an active flag (as set by update_cvc_flags)
+  /// \brief Number of CVC objects defined
-  inline size_t num_active_cvcs() const { return n_active_cvcs; }
+  inline size_t num_cvcs() const
+  {
+    return cvcs.size();
+  }
+
+  /// \brief number of CVC objects with an active flag (as set by
+  /// update_cvc_flags)
+  inline size_t num_active_cvcs() const
+  {
+    return n_active_cvcs;
+  }
 
   /// \brief Use the internal metrics (as from \link colvar::cvc
   /// \endlink objects) to calculate square distances and gradients
@@ -413,22 +438,20 @@ public:
   /// Handles correctly symmetries and periodic boundary conditions
   void wrap(colvarvalue &x_unwrapped) const;
 
-
   /// Read the analysis tasks
   int parse_analysis(std::string const &conf);
 
   /// Perform analysis tasks
   int analyze();
 
-
   /// Read the value from a collective variable trajectory file
   std::istream & read_traj(std::istream &is);
+
   /// Output formatted values to the trajectory file
   std::ostream & write_traj(std::ostream &os);
   /// Write a label to the trajectory file (comment line)
   std::ostream & write_traj_label(std::ostream &os);
 
-
   /// Read the collective variable from a restart file
   std::istream & read_restart(std::istream &is);
   /// Write the collective variable to a restart file
@@ -437,8 +460,8 @@ public:
   /// Write output files (if defined, e.g. in analysis mode)
   int write_output_files();
 
-
 protected:
+
   /// Previous value (to calculate velocities during analysis)
   colvarvalue            x_old;
 
@@ -530,11 +553,12 @@ protected:
   /// Calculate the running average and its standard deviation
   int calc_runave();
 
-  /// If extended Lagrangian active: colvar energies (kinetic and harmonic potential)
+  /// If extended Lagrangian active: colvar kinetic energy
   cvm::real kinetic_energy;
+  /// If extended Lagrangian active: colvar harmonic potential
   cvm::real potential_energy;
-public:
 
+public:
 
   // collective variable component base class
   class cvc;
@@ -577,6 +601,8 @@ public:
   class CVBasedPath;
   class gspathCV;
   class gzpathCV;
+  class aspathCV;
+  class azpathCV;
 
   // non-scalar components
   class distance_vec;
@@ -596,7 +622,6 @@ protected:
   /// in all cvcs (called when enabling f_cv_collect_gradients)
   void build_atom_list(void);
 
-private:
   /// Name of scripted function to be used
   std::string scripted_function;
 
@@ -620,6 +645,7 @@ private:
 #endif
 
 public:
+
   /// \brief Sorted array of (zero-based) IDs for all atoms involved
   std::vector<int> atom_ids;
 
@@ -628,34 +654,35 @@ public:
   /// For scalar variables only!
   std::vector<cvm::rvector> atomic_gradients;
 
-  inline size_t n_components() const {
-    return cvcs.size();
-  }
-
   /// \brief Get vector of vectors of atom IDs for all atom groups
   virtual std::vector<std::vector<int> > get_atom_lists();
 };
 
+
 inline cvm::real const & colvar::force_constant() const
 {
   return ext_force_k;
 }
 
+
 inline colvarvalue const & colvar::value() const
 {
   return x_reported;
 }
 
+
 inline colvarvalue const & colvar::actual_value() const
 {
   return x;
 }
 
+
 inline colvarvalue const & colvar::run_ave() const
 {
   return runave;
 }
 
+
 inline colvarvalue const & colvar::velocity() const
 {
   return v_reported;

lib/colvars/colvar_UIestimator.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvar_arithmeticpath.h

@@ -0,0 +1,129 @@
+#ifndef ARITHMETICPATHCV_H
+#define ARITHMETICPATHCV_H
+
+#include "colvarmodule.h"
+
+#include <vector>
+#include <cmath>
+#include <iostream>
+#include <limits>
+
+namespace ArithmeticPathCV {
+
+using std::vector;
+
+enum path_sz {S, Z};
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+class ArithmeticPathBase {
+public:
+    ArithmeticPathBase() {}
+    virtual ~ArithmeticPathBase() {}
+    virtual void initialize(size_t p_num_elements, size_t p_total_frames, double p_lambda, const vector<element_type>& p_element, const vector<double>& p_weights);
+    virtual void updateDistanceToReferenceFrames() = 0;
+    virtual void computeValue();
+    virtual void computeDerivatives();
+    virtual void compute();
+protected:
+    scalar_type lambda;
+    vector<scalar_type> weights;
+    size_t num_elements;
+    size_t total_frames;
+    vector< vector<element_type> > frame_element_distances;
+    scalar_type s;
+    scalar_type z;
+    vector<element_type> dsdx;
+    vector<element_type> dzdx;
+private:
+    // intermediate variables
+    vector<scalar_type> s_numerator_frame;
+    vector<scalar_type> s_denominator_frame;
+    scalar_type numerator_s;
+    scalar_type denominator_s;
+    scalar_type normalization_factor;
+};
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void ArithmeticPathBase<element_type, scalar_type, path_type>::initialize(size_t p_num_elements, size_t p_total_frames, double p_lambda, const vector<element_type>& p_element, const vector<double>& p_weights) {
+    lambda = p_lambda;
+    weights = p_weights;
+    num_elements = p_num_elements;
+    total_frames = p_total_frames;
+    frame_element_distances.resize(total_frames, p_element);
+    for (size_t i_frame = 0; i_frame < frame_element_distances.size(); ++i_frame) {
+        for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
+            frame_element_distances[i_frame][j_elem].reset();
+        }
+    }
+    s = scalar_type(0);
+    z = scalar_type(0);
+    dsdx = p_element;
+    dzdx = p_element;
+    s_numerator_frame.resize(total_frames, scalar_type(0));
+    s_denominator_frame.resize(total_frames, scalar_type(0));
+    numerator_s = scalar_type(0);
+    denominator_s = scalar_type(0);
+    normalization_factor = 1.0 / static_cast<scalar_type>(total_frames - 1);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void ArithmeticPathBase<element_type, scalar_type, path_type>::computeValue() {
+    updateDistanceToReferenceFrames();
+    numerator_s = scalar_type(0);
+    denominator_s = scalar_type(0);
+    for (size_t i_frame = 0; i_frame < frame_element_distances.size(); ++i_frame) {
+        scalar_type exponent_tmp = scalar_type(0);
+        for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
+            exponent_tmp += weights[j_elem] * frame_element_distances[i_frame][j_elem] * weights[j_elem] * frame_element_distances[i_frame][j_elem];
+        }
+        exponent_tmp = exponent_tmp * -1.0 * lambda;
+	// prevent underflow if the argument of cvm::exp is less than -708.4
+        if (exponent_tmp > -708.4) {
+            exponent_tmp = cvm::exp(exponent_tmp);
+        } else {
+            exponent_tmp = 0;
+        }
+        numerator_s += static_cast<scalar_type>(i_frame) * exponent_tmp;
+        denominator_s += exponent_tmp;
+        s_numerator_frame[i_frame] = static_cast<scalar_type>(i_frame) * exponent_tmp;
+        s_denominator_frame[i_frame] = exponent_tmp;
+    }
+    s = numerator_s / denominator_s * normalization_factor;
+    z = -1.0 / lambda * cvm::logn(denominator_s);
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void ArithmeticPathBase<element_type, scalar_type, path_type>::compute() {
+    computeValue();
+    computeDerivatives();
+}
+
+template <typename element_type, typename scalar_type, path_sz path_type>
+void ArithmeticPathBase<element_type, scalar_type, path_type>::computeDerivatives() {
+    for (size_t j_elem = 0; j_elem < num_elements; ++j_elem) {
+        element_type dsdxj_numerator_part1(dsdx[j_elem]);
+        element_type dsdxj_numerator_part2(dsdx[j_elem]);
+        element_type dzdxj_numerator(dsdx[j_elem]);
+        dsdxj_numerator_part1.reset();
+        dsdxj_numerator_part2.reset();
+        dzdxj_numerator.reset();
+        for (size_t i_frame = 0; i_frame < frame_element_distances.size(); ++i_frame) {
+            element_type derivative_tmp = -2.0 * lambda * weights[j_elem] * weights[j_elem] * frame_element_distances[i_frame][j_elem];
+            dsdxj_numerator_part1 += s_numerator_frame[i_frame] * derivative_tmp;
+            dsdxj_numerator_part2 += s_denominator_frame[i_frame] * derivative_tmp;
+            dzdxj_numerator += s_denominator_frame[i_frame] * derivative_tmp;
+        }
+        dsdxj_numerator_part1 *= denominator_s;
+        dsdxj_numerator_part2 *= numerator_s;
+        if ((dsdxj_numerator_part1 - dsdxj_numerator_part2).norm() < std::numeric_limits<scalar_type>::min()) {
+            dsdx[j_elem] = 0;
+        } else {
+            dsdx[j_elem] = (dsdxj_numerator_part1 - dsdxj_numerator_part2) / (denominator_s * denominator_s) * normalization_factor;
+        }
+        dzdx[j_elem] = -1.0 / lambda * dzdxj_numerator / denominator_s;
+    }
+}
+
+}
+
+#endif // ARITHMETICPATHCV_H

lib/colvars/colvar_geometricpath.h

@@ -2,12 +2,14 @@
 #define GEOMETRICPATHCV_H
 // 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
+// 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 "colvarmodule.h"
+
 #include <vector>
 #include <cmath>
 #include <iostream>
@@ -67,8 +69,8 @@ public:
     virtual ~GeometricPathBase() {}
     virtual void initialize(size_t vector_size, const element_type& element = element_type(), size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
     virtual void initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames = 1, bool p_use_second_closest_frame = true, bool p_use_third_closest_frame = false, bool p_use_z_square = false);
-    virtual void prepareVectors();
+    virtual void prepareVectors() = 0;
-    virtual void updateReferenceDistances();
+    virtual void updateDistanceToReferenceFrames() = 0;
     virtual void compute();
     virtual void determineClosestFrames();
     virtual void computeValue();
@@ -119,7 +121,7 @@ void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t
 }
 
 template <typename element_type, typename scalar_type, path_sz path_type>
-void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t vector_size, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
+void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t /* vector_size */, const std::vector<element_type>& elements, size_t total_frames, bool p_use_second_closest_frame, bool p_use_third_closest_frame, bool p_use_z_square) {
     v1v1 = scalar_type();
     v2v2 = scalar_type();
     v3v3 = scalar_type();
@@ -151,18 +153,6 @@ void GeometricPathBase<element_type, scalar_type, path_type>::initialize(size_t
     m = static_cast<scalar_type>(1.0);
 }
 
-template <typename element_type, typename scalar_type, path_sz path_type>
-void GeometricPathBase<element_type, scalar_type, path_type>::prepareVectors() {
-    std::cout << "Warning: you should not call the prepareVectors() in base class!\n";
-    std::cout << std::flush;
-}
-
-template <typename element_type, typename scalar_type, path_sz path_type>
-void GeometricPathBase<element_type, scalar_type, path_type>::updateReferenceDistances() {
-    std::cout << "Warning: you should not call the updateReferenceDistances() in base class!\n";
-    std::cout << std::flush;
-}
-
 template <typename element_type, typename scalar_type, path_sz path_type>
 void GeometricPathBase<element_type, scalar_type, path_type>::compute() {
     computeValue();
@@ -182,7 +172,7 @@ void GeometricPathBase<element_type, scalar_type, path_type>::determineClosestFr
         // sigma(z) is on the right side of the closest frame
         sign = -1;
     }
-    if (std::abs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
+    if (cvm::fabs(static_cast<long>(frame_index[0]) - static_cast<long>(frame_index[1])) > 1) {
         std::cout << "Warning: Geometrical pathCV relies on the assumption that the second closest frame is the neighbouring frame\n";
         std::cout << "         Please check your configuration or increase restraint on z(σ)\n";
         for (size_t i_frame = 0; i_frame < frame_index.size(); ++i_frame) {
@@ -197,7 +187,7 @@ void GeometricPathBase<element_type, scalar_type, path_type>::determineClosestFr
 
 template <typename element_type, typename scalar_type, path_sz path_type>
 void GeometricPathBase<element_type, scalar_type, path_type>::computeValue() {
-    updateReferenceDistances();
+    updateDistanceToReferenceFrames();
     determineClosestFrames();
     prepareVectors();
     v1v1 = scalar_type();
@@ -218,14 +208,14 @@ void GeometricPathBase<element_type, scalar_type, path_type>::computeValue() {
             v4v4 += v4[i_elem] * v4[i_elem];
         }
     }
-    f = (std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)) - v1v3) / v3v3;
+    f = (cvm::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)) - v1v3) / v3v3;
     if (path_type == Z) {
         dx = 0.5 * (f - 1);
         zz = v1v1 + 2 * dx * v1v4 + dx * dx * v4v4;
         if (use_z_square) {
             z = zz;
         } else {
-            z = std::sqrt(std::fabs(zz));
+            z = cvm::sqrt(cvm::fabs(zz));
         }
     }
     if (path_type == S) {
@@ -235,7 +225,7 @@ void GeometricPathBase<element_type, scalar_type, path_type>::computeValue() {
 
 template <typename element_type, typename scalar_type, path_sz path_type>
 void GeometricPathBase<element_type, scalar_type, path_type>::computeDerivatives() {
-    const scalar_type factor1 = 1.0 / (2.0 * v3v3 * std::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)));
+    const scalar_type factor1 = 1.0 / (2.0 * v3v3 * cvm::sqrt(v1v3 * v1v3 - v3v3 * (v1v1 - v2v2)));
     const scalar_type factor2 = 1.0 / v3v3;
     for (size_t i_elem = 0; i_elem < v1.size(); ++i_elem) {
         // Compute the derivative of f with vector v1

lib/colvars/colvaratoms.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -628,39 +628,42 @@ int cvm::atom_group::add_atom_numbers(std::string const &numbers_conf)
 
 int cvm::atom_group::add_index_group(std::string const &index_group_name)
 {
-  colvarmodule *cv = cvm::main();
+  std::vector<std::string> const &index_group_names =
+    cvm::main()->index_group_names;
+  std::vector<std::vector<int> *> const &index_groups =
+    cvm::main()->index_groups;
 
-  std::list<std::string>::iterator names_i = cv->index_group_names.begin();
+  size_t i_group = 0;
-  std::list<std::vector<int> >::iterator index_groups_i = cv->index_groups.begin();
+  for ( ; i_group < index_groups.size(); i_group++) {
-  for ( ; names_i != cv->index_group_names.end() ; ++names_i, ++index_groups_i) {
+    if (index_group_names[i_group] == index_group_name)
-    if (*names_i == index_group_name)
       break;
   }
 
-  if (names_i == cv->index_group_names.end()) {
+  if (i_group >= index_group_names.size()) {
-    cvm::error("Error: could not find index group "+
+    return cvm::error("Error: could not find index group "+
-               index_group_name+" among those provided by the index file.\n",
+                      index_group_name+" among those already provided.\n",
                       INPUT_ERROR);
-    return COLVARS_ERROR;
   }
 
-  atoms_ids.reserve(atoms_ids.size()+index_groups_i->size());
+  int error_code = COLVARS_OK;
+
+  std::vector<int> const &index_group = *(index_groups[i_group]);
+
+  atoms_ids.reserve(atoms_ids.size()+index_group.size());
 
   if (is_enabled(f_ag_scalable)) {
-    for (size_t i = 0; i < index_groups_i->size(); i++) {
+    for (size_t i = 0; i < index_group.size(); i++) {
-      add_atom_id((cvm::proxy)->check_atom_id((*index_groups_i)[i]));
+      error_code |=
+        add_atom_id((cvm::proxy)->check_atom_id(index_group[i]));
     }
   } else {
-    atoms.reserve(atoms.size()+index_groups_i->size());
+    atoms.reserve(atoms.size()+index_group.size());
-    for (size_t i = 0; i < index_groups_i->size(); i++) {
+    for (size_t i = 0; i < index_group.size(); i++) {
-      add_atom(cvm::atom((*index_groups_i)[i]));
+      error_code |= add_atom(cvm::atom(index_group[i]));
     }
   }
 
-  if (cvm::get_error())
+  return error_code;
-    return COLVARS_ERROR;
-
-  return COLVARS_OK;
 }
 
 

lib/colvars/colvaratoms.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvarbias.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -233,25 +233,18 @@ int colvarbias::add_colvar(std::string const &cv_name)
     }
 
     colvars.push_back(cv);
+    cv->biases.push_back(this); // add back-reference to this bias to colvar
+
+    // Add dependency link. All biases need at least the value of each colvar
+    // although possibly not at all timesteps
+    add_child(cv);
 
     colvar_forces.push_back(colvarvalue());
     colvar_forces.back().type(cv->value()); // make sure each force is initialized to zero
     colvar_forces.back().is_derivative(); // colvar constraints are not applied to the force
     colvar_forces.back().reset();
-
     previous_colvar_forces.push_back(colvar_forces.back());
 
-    cv->biases.push_back(this); // add back-reference to this bias to colvar
-
-    if (is_enabled(f_cvb_apply_force)) {
-      cv->enable(f_cv_gradient);
-    }
-
-    // Add dependency link.
-    // All biases need at least the value of each colvar
-    // although possibly not at all timesteps
-    add_child(cv);
-
   } else {
     cvm::error("Error: cannot find a colvar named \""+
                cv_name+"\".\n", INPUT_ERROR);
@@ -268,13 +261,29 @@ int colvarbias::update()
     cvm::log("Updating the "+bias_type+" bias \""+this->name+"\".\n");
   }
 
+  int error_code = COLVARS_OK;
+
   has_data = true;
 
+  error_code |= calc_energy(NULL);
+  error_code |= calc_forces(NULL);
+
+  return error_code;
+}
+
+
+int colvarbias::calc_energy(std::vector<colvarvalue> const *)
+{
   bias_energy = 0.0;
+  return COLVARS_OK;
+}
+
+
+int colvarbias::calc_forces(std::vector<colvarvalue> const *)
+{
   for (size_t ir = 0; ir < num_variables(); ir++) {
     colvar_forces[ir].reset();
   }
-
   return COLVARS_OK;
 }
 
@@ -309,7 +318,7 @@ int colvarbias::end_of_step()
 }
 
 
-int colvarbias::change_configuration(std::string const &conf)
+int colvarbias::change_configuration(std::string const & /* conf */)
 {
   cvm::error("Error: change_configuration() not implemented.\n",
              COLVARS_NOT_IMPLEMENTED);
@@ -317,7 +326,7 @@ int colvarbias::change_configuration(std::string const &conf)
 }
 
 
-cvm::real colvarbias::energy_difference(std::string const &conf)
+cvm::real colvarbias::energy_difference(std::string const & /* conf */)
 {
   cvm::error("Error: energy_difference() not implemented.\n",
              COLVARS_NOT_IMPLEMENTED);
@@ -336,7 +345,7 @@ int colvarbias::current_bin()
   cvm::error("Error: current_bin() not implemented.\n");
   return COLVARS_NOT_IMPLEMENTED;
 }
-int colvarbias::bin_count(int bin_index)
+int colvarbias::bin_count(int /* bin_index */)
 {
   cvm::error("Error: bin_count() not implemented.\n");
   return COLVARS_NOT_IMPLEMENTED;
@@ -410,6 +419,8 @@ std::istream & colvarbias::read_state(std::istream &is)
        !(is >> brace) || !(brace == "{") ||
        !(is >> colvarparse::read_block("configuration", conf)) ||
        (set_state_params(conf) != COLVARS_OK) ) {
+    if (key != bias_type)
+      cvm::log("Found key \"" + key + "\" instead of \"" + bias_type + "\"\n");
     cvm::error("Error: in reading state configuration for \""+bias_type+"\" bias \""+
                this->name+"\" at position "+
                cvm::to_str(static_cast<size_t>(is.tellg()))+
@@ -646,7 +657,7 @@ std::string const colvarbias_ti::get_state_params() const
 }
 
 
-int colvarbias_ti::set_state_params(std::string const &state_conf)
+int colvarbias_ti::set_state_params(std::string const & /* state_conf */)
 {
   return COLVARS_OK;
 }

lib/colvars/colvarbias.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -51,17 +51,18 @@ public:
   }
 
   /// Retrieve colvar values and calculate their biasing forces
-  /// Return bias energy
+  /// Some implementations may use calc_energy() and calc_forces()
   virtual int update();
 
-  /// \brief Compute the energy of the bias with alternative values of the
+  /// Compute the energy of the bias
-  /// collective variables (suitable for bias exchange)
+  /// Uses the vector of colvar values provided if not NULL, and the values
-  virtual int calc_energy(std::vector<colvarvalue> const &values =
+  /// currently cached in the bias instance otherwise
-                          std::vector<colvarvalue>(0))
+  virtual int calc_energy(std::vector<colvarvalue> const *values);
-  {
+
-    cvm::error("Error: calc_energy() not implemented.\n", COLVARS_NOT_IMPLEMENTED);
+  /// Compute the forces due to the bias
-    return COLVARS_NOT_IMPLEMENTED;
+  /// Uses the vector of colvar values provided if not NULL, and the values
-  }
+  /// currently cached in the bias instance otherwise
+  virtual int calc_forces(std::vector<colvarvalue> const *values);
 
   /// Send forces to the collective variables
   virtual void communicate_forces();

lib/colvars/colvarbias_abf.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -35,6 +35,8 @@ int colvarbias_abf::init(std::string const &conf)
 {
   colvarbias::init(conf);
 
+  colvarproxy *proxy = cvm::main()->proxy;
+
   enable(f_cvb_scalar_variables);
   enable(f_cvb_calc_pmf);
 
@@ -76,11 +78,13 @@ int colvarbias_abf::init(std::string const &conf)
   // shared ABF
   get_keyval(conf, "shared", shared_on, false);
   if (shared_on) {
-    if (!cvm::replica_enabled() || cvm::replica_num() <= 1) {
+    if ((proxy->replica_enabled() != COLVARS_OK) ||
-      cvm::error("Error: shared ABF requires more than one replica.");
+        (proxy->num_replicas() <= 1)) {
-      return COLVARS_ERROR;
+      return cvm::error("Error: shared ABF requires more than one replica.",
+                        INPUT_ERROR);
     }
-    cvm::log("shared ABF will be applied among "+ cvm::to_str(cvm::replica_num()) + " replicas.\n");
+    cvm::log("shared ABF will be applied among "+
+             cvm::to_str(proxy->num_replicas()) + " replicas.\n");
     if (cvm::proxy->smp_enabled() == COLVARS_OK) {
       cvm::error("Error: shared ABF is currently not available with SMP parallelism; "
                  "please set \"SMP off\" at the top of the Colvars configuration file.\n",
@@ -483,13 +487,18 @@ int colvarbias_abf::update()
     eabf_UI.update(cvm::step_absolute(), x, y);
   }
 
+  /// Add the bias energy for 1D ABF
+  bias_energy = calc_energy(NULL);
+
   return COLVARS_OK;
 }
 
 
 int colvarbias_abf::replica_share() {
 
-  if ( !cvm::replica_enabled() ) {
+  colvarproxy *proxy = cvm::main()->proxy;
+
+  if (proxy->replica_enabled() != COLVARS_OK) {
     cvm::error("Error: shared ABF: No replicas.\n");
     return COLVARS_ERROR;
   }
@@ -508,12 +517,12 @@ int colvarbias_abf::replica_share() {
   size_t msg_total = data_n*sizeof(size_t) + samp_start;
   char* msg_data = new char[msg_total];
 
-  if (cvm::replica_index() == 0) {
+  if (proxy->replica_index() == 0) {
     int p;
     // Replica 0 collects the delta gradient and count from the others.
-    for (p = 1; p < cvm::replica_num(); p++) {
+    for (p = 1; p < proxy->num_replicas(); p++) {
       // Receive the deltas.
-      cvm::replica_comm_recv(msg_data, msg_total, p);
+      proxy->replica_comm_recv(msg_data, msg_total, p);
 
       // Map the deltas from the others into the grids.
       last_gradients->raw_data_in((cvm::real*)(&msg_data[0]));
@@ -528,8 +537,8 @@ int colvarbias_abf::replica_share() {
     // Now we must send the combined gradient to the other replicas.
     gradients->raw_data_out((cvm::real*)(&msg_data[0]));
     samples->raw_data_out((size_t*)(&msg_data[samp_start]));
-    for (p = 1; p < cvm::replica_num(); p++) {
+    for (p = 1; p < proxy->num_replicas(); p++) {
-      cvm::replica_comm_send(msg_data, msg_total, p);
+      proxy->replica_comm_send(msg_data, msg_total, p);
     }
 
   } else {
@@ -541,10 +550,10 @@ int colvarbias_abf::replica_share() {
     // Cast the raw char data to the gradient and samples.
     last_gradients->raw_data_out((cvm::real*)(&msg_data[0]));
     last_samples->raw_data_out((size_t*)(&msg_data[samp_start]));
-    cvm::replica_comm_send(msg_data, msg_total, 0);
+    proxy->replica_comm_send(msg_data, msg_total, 0);
 
     // We now receive the combined gradient from Replica 0.
-    cvm::replica_comm_recv(msg_data, msg_total, 0);
+    proxy->replica_comm_recv(msg_data, msg_total, 0);
     // We sync to the combined gradient computed by Replica 0.
     gradients->raw_data_in((cvm::real*)(&msg_data[0]));
     samples->raw_data_in((size_t*)(&msg_data[samp_start]));
@@ -552,7 +561,7 @@ int colvarbias_abf::replica_share() {
 
   // Without a barrier it's possible that one replica starts
   // share 2 when other replicas haven't finished share 1.
-  cvm::replica_comm_barrier();
+  proxy->replica_comm_barrier();
   // Done syncing the replicas.
   delete[] msg_data;
 
@@ -832,3 +841,50 @@ int colvarbias_abf::write_output_files()
   write_gradients_samples(output_prefix);
   return COLVARS_OK;
 }
+
+int colvarbias_abf::calc_energy(std::vector<colvarvalue> const *values)
+{
+  if (values) {
+    return cvm::error("colvarbias_abf::calc_energy() with an argument "
+                      "is currently not implemented.\n",
+                      COLVARS_NOT_IMPLEMENTED);
+  }
+
+  if (num_variables() != 1) return 0.0;
+
+  // Get the home bin.
+  int home0 = gradients->current_bin_scalar(0);
+  if (home0 < 0) return 0.0;
+  int gradient_len = (int)(gradients->number_of_points(0));
+  int home = (home0 < gradient_len) ? home0 : (gradient_len-1);
+
+  // Integrate the gradient up to the home bin.
+  cvm::real sum = 0.0;
+  for (int i = 0; i < home; i++) {
+    std::vector<int> ix(1,i);
+
+    // Include the full_samples factor if necessary.
+    unsigned int count = samples->value(ix);
+    cvm::real fact = 1.0;
+    if ( count < full_samples ) {
+      fact = (count < min_samples) ? 0.0 :
+        (cvm::real(count - min_samples)) / (cvm::real(full_samples - min_samples));
+    }
+    if (count > 0) sum += fact*gradients->value(ix)/count*gradients->widths[0];
+  }
+
+  // Integrate the gradient up to the current position in the home interval, a fractional portion of a bin.
+  std::vector<int> ix(1,home);
+  cvm::real frac = gradients->current_bin_scalar_fraction(0);
+  unsigned int count = samples->value(ix);
+  cvm::real fact = 1.0;
+  if ( count < full_samples ) {
+    fact = (count < min_samples) ? 0.0 :
+      (cvm::real(count - min_samples)) / (cvm::real(full_samples - min_samples));
+  }
+  if (count > 0)
+    sum += fact*gradients->value(ix)/count*gradients->widths[0]*frac;
+
+  // The applied potential is the negative integral of force samples.
+  return -sum;
+}

lib/colvars/colvarbias_abf.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -159,7 +159,9 @@ private:
   virtual std::istream& read_state_data(std::istream&);
   virtual std::ostream& write_state_data(std::ostream&);
   virtual int write_output_files();
+
+  /// Calculate the bias energy for 1D ABF
+  virtual int calc_energy(std::vector<colvarvalue> const *values);
 };
 
 #endif
-

lib/colvars/colvarbias_alb.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -255,14 +255,12 @@ int colvarbias_alb::set_state_params(std::string const &conf)
   if (!get_keyval(conf, "maxCouplingRange", max_coupling_range))
     cvm::fatal_error("Error: maxCouplingRange  is missing from the restart.\n");
 
-
   if (!get_keyval(conf, "couplingRate", coupling_rate))
     cvm::fatal_error("Error: current setCoupling  is missing from the restart.\n");
 
   if (!get_keyval(conf, "couplingAccum", coupling_accum))
     cvm::fatal_error("Error: couplingAccum is missing from the restart.\n");
 
-
   if (!get_keyval(conf, "mean", means))
     cvm::fatal_error("Error: current mean is missing from the restart.\n");
 
@@ -388,7 +386,7 @@ std::ostream & colvarbias_alb::write_traj(std::ostream &os)
     for (size_t i = 0; i < means.size(); i++) {
       os << " "
          << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
-         << -2. * (means[i] / (static_cast<cvm::real> (colvar_centers[i])) - 1) * ssd[i] / (fmax(update_calls,2) - 1);
+         << -2.0 * (means[i] / (static_cast<cvm::real>(colvar_centers[i])) - 1) * ssd[i] / (fmax(update_calls, 2.0) - 1);
 
     }
 
@@ -405,8 +403,8 @@ cvm::real colvarbias_alb::restraint_potential(cvm::real k,
 
 
 colvarvalue colvarbias_alb::restraint_force(cvm::real k,
-                                            colvar const *x,
+                                            colvar const * /* x */,
-                                            colvarvalue const &xcenter) const
+                                            colvarvalue const & /* xcenter */) const
 {
   return k;
 }

lib/colvars/colvarbias_alb.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvarbias_histogram.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -78,7 +78,7 @@ int colvarbias_histogram::init(std::string const &conf)
   }
 
   for (i = 0; i < num_variables(); i++) {
-    colvars[i]->enable(f_cv_grid);
+    colvars[i]->enable(f_cv_grid); // Could be a child dependency of a f_cvb_use_grids feature
   }
 
   grid = new colvar_grid_scalar();

lib/colvars/colvarbias_histogram.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvarbias_meta.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -38,14 +38,29 @@ colvarbias_meta::colvarbias_meta(char const *key)
   new_hills_begin = hills.end();
   hills_traj_os = NULL;
 
+  use_grids = true;
+  rebin_grids = false;
+  hills_energy = NULL;
+  hills_energy_gradients = NULL;
+
+  dump_fes = true;
+  keep_hills = false;
+  dump_fes_save = false;
+  dump_replica_fes = false;
+
   ebmeta_equil_steps = 0L;
+
+  replica_update_freq = 0;
+  replica_id.clear();
 }
 
 
 int colvarbias_meta::init(std::string const &conf)
 {
-  colvarbias::init(conf);
+  int error_code = COLVARS_OK;
-  colvarbias_ti::init(conf);
+
+  error_code |= colvarbias::init(conf);
+  error_code |= colvarbias_ti::init(conf);
 
   enable(f_cvb_calc_pmf);
 
@@ -77,21 +92,16 @@ int colvarbias_meta::init(std::string const &conf)
       comm = single_replica;
   }
 
-  // in all cases, the first replica is this bias itself
+  get_keyval(conf, "useGrids", use_grids, use_grids);
-  if (replicas.size() == 0) {
-    replicas.push_back(this);
-  }
-
-  get_keyval(conf, "useGrids", use_grids, true);
 
   if (use_grids) {
     get_keyval(conf, "gridsUpdateFrequency", grids_freq, new_hill_freq);
-    get_keyval(conf, "rebinGrids", rebin_grids, false);
+    get_keyval(conf, "rebinGrids", rebin_grids, rebin_grids);
 
     expand_grids = false;
     size_t i;
     for (i = 0; i < num_variables(); i++) {
-      variables(i)->enable(f_cv_grid);
+      variables(i)->enable(f_cv_grid); // Could be a child dependency of a f_cvb_use_grids feature
       if (variables(i)->expand_boundaries) {
         expand_grids = true;
         cvm::log("Metadynamics bias \""+this->name+"\""+
@@ -101,67 +111,24 @@ int colvarbias_meta::init(std::string const &conf)
       }
     }
 
-    get_keyval(conf, "keepHills", keep_hills, false);
+    get_keyval(conf, "writeFreeEnergyFile", dump_fes, dump_fes);
-    if (! get_keyval(conf, "writeFreeEnergyFile", dump_fes, true))
+
-      get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
+    get_keyval(conf, "keepHills", keep_hills, keep_hills);
-    if (get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false, colvarparse::parse_silent)) {
-      cvm::log("Option \"saveFreeEnergyFile\" is deprecated, "
-               "please use \"keepFreeEnergyFiles\" instead.");
-    }
     get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save);
 
     hills_energy           = new colvar_grid_scalar(colvars);
     hills_energy_gradients = new colvar_grid_gradient(colvars);
+
   } else {
-    rebin_grids = false;
+
-    keep_hills = false;
     dump_fes = false;
-    dump_fes_save = false;
-    dump_replica_fes = false;
-
-    hills_energy           = NULL;
-    hills_energy_gradients = NULL;
-  }
-
-  if (comm != single_replica) {
-
-    if (expand_grids)
-      cvm::fatal_error("Error: expandBoundaries is not supported when "
-                       "using more than one replicas; please allocate "
-                       "wide enough boundaries for each colvar"
-                       "ahead of time.\n");
-
-    if (get_keyval(conf, "dumpPartialFreeEnergyFile", dump_replica_fes, false)) {
-      if (dump_replica_fes && (! dump_fes)) {
-        cvm::log("Enabling \"dumpFreeEnergyFile\".\n");
-      }
-    }
-
-    get_keyval(conf, "replicaID", replica_id, std::string(""));
-    if (!replica_id.size())
-      cvm::error("Error: replicaID must be defined "
-                 "when using more than one replica.\n", INPUT_ERROR);
-
-    get_keyval(conf, "replicasRegistry",
-               replicas_registry_file,
-               (this->name+".replicas.registry.txt"));
-
-    get_keyval(conf, "replicaUpdateFrequency",
-               replica_update_freq, new_hill_freq);
-
-    if (keep_hills)
-      cvm::log("Warning: in metadynamics bias \""+this->name+"\""+
-               ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
-               ": keepHills with more than one replica can lead to a very "
-               "large amount of input/output and slow down your calculations.  "
-               "Please consider disabling it.\n");
-
   }
 
   get_keyval(conf, "writeHillsTrajectory", b_hills_traj, false);
 
-  init_well_tempered_params(conf);
+  error_code |= init_replicas_params(conf);
-  init_ebmeta_params(conf);
+  error_code |= init_well_tempered_params(conf);
+  error_code |= init_ebmeta_params(conf);
 
   if (cvm::debug())
     cvm::log("Done initializing the metadynamics bias \""+this->name+"\""+
@@ -171,6 +138,72 @@ int colvarbias_meta::init(std::string const &conf)
 }
 
 
+int colvarbias_meta::init_replicas_params(std::string const &conf)
+{
+  colvarproxy *proxy = cvm::main()->proxy;
+
+  // in all cases, the first replica is this bias itself
+  if (replicas.size() == 0) {
+    replicas.push_back(this);
+  }
+
+  if (comm != single_replica) {
+
+    if (!get_keyval(conf, "writePartialFreeEnergyFile",
+                    dump_replica_fes, dump_replica_fes)) {
+      get_keyval(conf, "dumpPartialFreeEnergyFile", dump_replica_fes,
+                 dump_replica_fes, colvarparse::parse_silent);
+    }
+
+    if (dump_replica_fes && (! dump_fes)) {
+      dump_fes = true;
+      cvm::log("Enabling \"writeFreeEnergyFile\".\n");
+    }
+
+    get_keyval(conf, "replicaID", replica_id, replica_id);
+    if (!replica_id.size()) {
+      if (proxy->replica_enabled() == COLVARS_OK) {
+        // Obtain replicaID from the communicator
+        replica_id = cvm::to_str(proxy->replica_index());
+        cvm::log("Setting replicaID from communication layer: replicaID = "+
+                 replica_id+".\n");
+      } else {
+        return cvm::error("Error: using more than one replica, but replicaID "
+                          "could not be obtained.\n", INPUT_ERROR);
+      }
+    }
+
+    get_keyval(conf, "replicasRegistry", replicas_registry_file,
+               replicas_registry_file);
+    if (!replicas_registry_file.size()) {
+      return cvm::error("Error: the name of the \"replicasRegistry\" file "
+                        "must be provided.\n", INPUT_ERROR);
+    }
+
+    get_keyval(conf, "replicaUpdateFrequency",
+               replica_update_freq, replica_update_freq);
+    if (replica_update_freq == 0) {
+      return cvm::error("Error: replicaUpdateFrequency must be positive.\n",
+                        INPUT_ERROR);
+    }
+
+    if (expand_grids) {
+      return cvm::error("Error: expandBoundaries is not supported when "
+                        "using more than one replicas; please allocate "
+                        "wide enough boundaries for each colvar"
+                        "ahead of time.\n", INPUT_ERROR);
+    }
+
+    if (keep_hills) {
+      return cvm::error("Error: multipleReplicas and keepHills are not "
+                        "supported together.\n", INPUT_ERROR);
+    }
+  }
+
+  return COLVARS_OK;
+}
+
+
 int colvarbias_meta::init_well_tempered_params(std::string const &conf)
 {
   // for well-tempered metadynamics
@@ -379,8 +412,8 @@ int colvarbias_meta::update()
     error_code |= replica_share();
   }
 
-  error_code |= calc_energy();
+  error_code |= calc_energy(NULL);
-  error_code |= calc_forces();
+  error_code |= calc_forces(NULL);
 
   return error_code;
 }
@@ -418,7 +451,7 @@ int colvarbias_meta::update_grid_params()
         int       &new_size = new_sizes[i];
         bool changed_lb = false, changed_ub = false;
 
-        if (!variables(i)->hard_lower_boundary)
+        if (!variables(i)->is_enabled(f_cv_hard_lower_boundary))
           if (curr_bin[i] < min_buffer) {
             int const extra_points = (min_buffer - curr_bin[i]);
             new_lb -= extra_points * variables(i)->width;
@@ -435,7 +468,7 @@ int colvarbias_meta::update_grid_params()
                      cvm::to_str(new_lower_boundaries[i])+".\n");
           }
 
-        if (!variables(i)->hard_upper_boundary)
+        if (!variables(i)->is_enabled(f_cv_hard_upper_boundary))
           if (curr_bin[i] > new_size - min_buffer - 1) {
             int const extra_points = (curr_bin[i] - (new_size - 1) + min_buffer);
             new_ub += extra_points * variables(i)->width;
@@ -521,7 +554,7 @@ int colvarbias_meta::update_bias()
         std::vector<int> curr_bin = hills_energy->get_colvars_index();
         hills_energy_sum_here = hills_energy->value(curr_bin);
       } else {
-        calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here);
+        calc_hills(new_hills_begin, hills.end(), hills_energy_sum_here, NULL);
       }
       hills_scale *= cvm::exp(-1.0*hills_energy_sum_here/(bias_temperature*cvm::boltzmann()));
     }
@@ -578,7 +611,7 @@ int colvarbias_meta::update_grid_data()
 }
 
 
-int colvarbias_meta::calc_energy(std::vector<colvarvalue> const &values)
+int colvarbias_meta::calc_energy(std::vector<colvarvalue> const *values)
 {
   size_t ir = 0;
 
@@ -586,8 +619,8 @@ int colvarbias_meta::calc_energy(std::vector<colvarvalue> const &values)
     replicas[ir]->bias_energy = 0.0;
   }
 
-  std::vector<int> const curr_bin = values.size() ?
+  std::vector<int> const curr_bin = values ?
-    hills_energy->get_colvars_index(values) :
+    hills_energy->get_colvars_index(*values) :
     hills_energy->get_colvars_index();
 
   if (hills_energy->index_ok(curr_bin)) {
@@ -619,7 +652,8 @@ int colvarbias_meta::calc_energy(std::vector<colvarvalue> const &values)
   for (ir = 0; ir < replicas.size(); ir++) {
     calc_hills(replicas[ir]->new_hills_begin,
                replicas[ir]->hills.end(),
-               bias_energy);
+               bias_energy,
+               values);
     if (cvm::debug()) {
       cvm::log("Hills energy = "+cvm::to_str(bias_energy)+".\n");
     }
@@ -629,7 +663,7 @@ int colvarbias_meta::calc_energy(std::vector<colvarvalue> const &values)
 }
 
 
-int colvarbias_meta::calc_forces(std::vector<colvarvalue> const &values)
+int colvarbias_meta::calc_forces(std::vector<colvarvalue> const *values)
 {
   size_t ir = 0, ic = 0;
   for (ir = 0; ir < replicas.size(); ir++) {
@@ -638,8 +672,8 @@ int colvarbias_meta::calc_forces(std::vector<colvarvalue> const &values)
     }
   }
 
-  std::vector<int> const curr_bin = values.size() ?
+  std::vector<int> const curr_bin = values ?
-    hills_energy->get_colvars_index(values) :
+    hills_energy->get_colvars_index(*values) :
     hills_energy->get_colvars_index();
 
   if (hills_energy->index_ok(curr_bin)) {
@@ -693,7 +727,7 @@ int colvarbias_meta::calc_forces(std::vector<colvarvalue> const &values)
 void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter      h_first,
                                  colvarbias_meta::hill_iter      h_last,
                                  cvm::real                      &energy,
-                                 std::vector<colvarvalue> const &colvar_values)
+                                 std::vector<colvarvalue> const *values)
 {
   size_t i = 0;
   std::vector<colvarvalue> curr_values(num_variables());
@@ -701,9 +735,9 @@ void colvarbias_meta::calc_hills(colvarbias_meta::hill_iter      h_first,
     curr_values[i].type(variables(i)->value());
   }
 
-  if (colvar_values.size()) {
+  if (values) {
     for (i = 0; i < num_variables(); i++) {
-      curr_values[i] = colvar_values[i];
+      curr_values[i] = (*values)[i];
     }
   } else {
     for (i = 0; i < num_variables(); i++) {
@@ -738,10 +772,10 @@ void colvarbias_meta::calc_hills_force(size_t const &i,
                                        colvarbias_meta::hill_iter      h_first,
                                        colvarbias_meta::hill_iter      h_last,
                                        std::vector<colvarvalue>       &forces,
-                                       std::vector<colvarvalue> const &values)
+                                       std::vector<colvarvalue> const *values)
 {
   // Retrieve the value of the colvar
-  colvarvalue const x(values.size() ? values[i] : variables(i)->value());
+  colvarvalue const x(values ? (*values)[i] : variables(i)->value());
 
   // do the type check only once (all colvarvalues in the hills series
   // were already saved with their types matching those in the
@@ -846,12 +880,12 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter  h_first,
 
       // loop over the hills and increment the energy grid locally
       hills_energy_here = 0.0;
-      calc_hills(h_first, h_last, hills_energy_here, colvar_values);
+      calc_hills(h_first, h_last, hills_energy_here, &colvar_values);
       he->acc_value(he_ix, hills_energy_here);
 
       for (i = 0; i < num_variables(); i++) {
         hills_forces_here[i].reset();
-        calc_hills_force(i, h_first, h_last, hills_forces_here, colvar_values);
+        calc_hills_force(i, h_first, h_last, hills_forces_here, &colvar_values);
         colvar_forces_scalar[i] = hills_forces_here[i].real_value;
       }
       hg->acc_force(hg_ix, &(colvar_forces_scalar.front()));
@@ -883,7 +917,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter  h_first,
       }
 
       hills_energy_here = 0.0;
-      calc_hills(h_first, h_last, hills_energy_here, colvar_values);
+      calc_hills(h_first, h_last, hills_energy_here, &colvar_values);
       he->acc_value(he_ix, hills_energy_here);
 
       he->incr(he_ix);
@@ -915,7 +949,7 @@ void colvarbias_meta::project_hills(colvarbias_meta::hill_iter  h_first,
 
 void colvarbias_meta::recount_hills_off_grid(colvarbias_meta::hill_iter  h_first,
                                              colvarbias_meta::hill_iter  h_last,
-                                             colvar_grid_scalar         *he)
+                                             colvar_grid_scalar         * /* he */)
 {
   hills_off_grid.clear();
 
@@ -985,11 +1019,6 @@ void colvarbias_meta::update_replicas_registry()
 
       if (new_replica == this->replica_id) {
         // this is the record for this same replica, skip it
-        if (cvm::debug())
-          cvm::log("Metadynamics bias \""+this->name+"\""+
-                   ((comm != single_replica) ? ", replica \""+replica_id+"\"" : "")+
-                   ": skipping this replica's own record: \""+
-                   new_replica+"\", \""+new_replica_file+"\"\n");
         new_replica_file.clear();
         new_replica.clear();
         continue;
@@ -1039,11 +1068,12 @@ void colvarbias_meta::update_replicas_registry()
           (replicas.back())->enable(f_cvb_calc_ti_samples);
           (replicas.back())->colvarbias_ti::init_grids();
         }
+        (replicas.back())->update_status = 1;
       }
     }
   } else {
-    cvm::fatal_error("Error: cannot read the replicas registry file \""+
+    cvm::error("Error: cannot read the replicas registry file \""+
-                     replicas_registry+"\".\n");
+               replicas_registry+"\".\n", FILE_ERROR);
   }
 
   // now (re)read the list file of each replica
@@ -1068,7 +1098,6 @@ void colvarbias_meta::update_replicas_registry()
                cvm::to_str(replica_update_freq)+" steps.\n");
       (replicas[ir])->update_status++;
     } else {
-      (replicas[ir])->update_status = 0;
       if (new_state_file != (replicas[ir])->replica_state_file) {
         cvm::log("Metadynamics bias \""+this->name+"\""+
                  ": replica \""+(replicas[ir])->replica_id+
@@ -1092,27 +1121,41 @@ void colvarbias_meta::read_replica_files()
   // Note: we start from the 2nd replica.
   for (size_t ir = 1; ir < replicas.size(); ir++) {
 
-    if (! (replicas[ir])->replica_state_file_in_sync) {
-      // if a new state file is being read, the hills file is also new
-      (replicas[ir])->replica_hills_file_pos = 0;
-    }
-
     // (re)read the state file if necessary
     if ( (! (replicas[ir])->has_data) ||
          (! (replicas[ir])->replica_state_file_in_sync) ) {
-
+      if ((replicas[ir])->replica_state_file.size()) {
         cvm::log("Metadynamics bias \""+this->name+"\""+
                  ": reading the state of replica \""+
                  (replicas[ir])->replica_id+"\" from file \""+
                  (replicas[ir])->replica_state_file+"\".\n");
-
         std::ifstream is((replicas[ir])->replica_state_file.c_str());
         if ((replicas[ir])->read_state(is)) {
           // state file has been read successfully
           (replicas[ir])->replica_state_file_in_sync = true;
           (replicas[ir])->update_status = 0;
+        } else {
+          cvm::log("Failed to read the file \""+
+                   (replicas[ir])->replica_state_file+
+                   "\": will try again in "+
+                   cvm::to_str(replica_update_freq)+" steps.\n");
+          (replicas[ir])->replica_state_file_in_sync = false;
+          (replicas[ir])->update_status++;
         }
         is.close();
+      } else {
+        cvm::log("Metadynamics bias \""+this->name+"\""+
+                 ": the state file of replica \""+
+                 (replicas[ir])->replica_id+"\" is currently undefined: "
+                 "will try again after "+
+                 cvm::to_str(replica_update_freq)+" steps.\n");
+        (replicas[ir])->update_status++;
+      }
+    }
+
+    if (! (replicas[ir])->replica_state_file_in_sync) {
+      // if a new state file is being read, the hills file is also new
+      (replicas[ir])->replica_hills_file_pos = 0;
     }
 
     // now read the hills added after writing the state file
@@ -1124,14 +1167,16 @@ void colvarbias_meta::read_replica_files()
                  (replicas[ir])->replica_id+"\" in the file \""+
                  (replicas[ir])->replica_hills_file+"\".\n");
 
-      // read hills from the other replicas' files; for each file, resume
+      // read hills from the other replicas' files
-      // the position recorded previously
 
       std::ifstream is((replicas[ir])->replica_hills_file.c_str());
       if (is.is_open()) {
 
-        // try to resume the previous position
+        // try to resume the previous position (if not the beginning)
+        if ((replicas[ir])->replica_hills_file_pos > 0) {
           is.seekg((replicas[ir])->replica_hills_file_pos, std::ios::beg);
+        }
+
         if (!is.is_open()){
           // if fail (the file may have been overwritten), reset this
           // position
@@ -1149,7 +1194,6 @@ void colvarbias_meta::read_replica_files()
         } else {
 
           while ((replicas[ir])->read_hill(is)) {
-            //           if (cvm::debug())
             cvm::log("Metadynamics bias \""+this->name+"\""+
                      ": received a hill from replica \""+
                      (replicas[ir])->replica_id+
@@ -1159,11 +1203,13 @@ void colvarbias_meta::read_replica_files()
           is.clear();
           // store the position for the next read
           (replicas[ir])->replica_hills_file_pos = is.tellg();
-          if (cvm::debug())
+          if (cvm::debug()) {
             cvm::log("Metadynamics bias \""+this->name+"\""+
-                     ": stopped reading file \""+(replicas[ir])->replica_hills_file+
+                     ": stopped reading file \""+
+                     (replicas[ir])->replica_hills_file+
                      "\" at position "+
                      cvm::to_str((replicas[ir])->replica_hills_file_pos)+".\n");
+          }
 
           // test whether this is the end of the file
           is.seekg(0, std::ios::end);
@@ -1175,12 +1221,11 @@ void colvarbias_meta::read_replica_files()
         }
 
       } else {
-        cvm::log("Failed to read the file \""+(replicas[ir])->replica_hills_file+
+        cvm::log("Failed to read the file \""+
+                 (replicas[ir])->replica_hills_file+
                  "\": will try again in "+
                  cvm::to_str(replica_update_freq)+" steps.\n");
         (replicas[ir])->update_status++;
-        // cvm::fatal_error ("Error: cannot read from file \""+
-        //                   (replicas[ir])->replica_hills_file+"\".\n");
       }
       is.close();
     }
@@ -1188,8 +1233,8 @@ void colvarbias_meta::read_replica_files()
     size_t const n_flush = (replica_update_freq/new_hill_freq + 1);
     if ((replicas[ir])->update_status > 3*n_flush) {
       // TODO: suspend the calculation?
-      cvm::log("WARNING: in metadynamics bias \""+this->name+"\""+
+      cvm::log("WARNING: metadynamics bias \""+this->name+"\""+
-               " failed to read completely the output of replica \""+
+               " could not read information from replica \""+
                (replicas[ir])->replica_id+
                "\" after more than "+
                cvm::to_str((replicas[ir])->update_status * replica_update_freq)+
@@ -1712,7 +1757,7 @@ void colvarbias_meta::write_pmf()
          cvm:: real target_val=target_dist->value(i);
          if (target_val>0) {
            pmf_val=pmf->value(i);
-           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
+           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
          }
          pmf->set_value(i,pmf_val);
       }
@@ -1753,7 +1798,7 @@ void colvarbias_meta::write_pmf()
          cvm:: real target_val=target_dist->value(i);
          if (target_val>0) {
            pmf_val=pmf->value(i);
-           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * std::log(target_val);
+           pmf_val=pmf_val+cvm::temperature() * cvm::boltzmann() * cvm::logn(target_val);
          }
          pmf->set_value(i,pmf_val);
       }

lib/colvars/colvarbias_meta.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -41,6 +41,7 @@ public:
   virtual ~colvarbias_meta();
 
   virtual int init(std::string const &conf);
+  virtual int init_replicas_params(std::string const &conf);
   virtual int init_well_tempered_params(std::string const &conf);
   virtual int init_ebmeta_params(std::string const &conf);
 
@@ -52,10 +53,8 @@ public:
   virtual int update_grid_data();
   virtual int replica_share();
 
-  virtual int calc_energy(std::vector<colvarvalue> const &values =
+  virtual int calc_energy(std::vector<colvarvalue> const *values);
-                          std::vector<colvarvalue>(0));
+  virtual int calc_forces(std::vector<colvarvalue> const *values);
-  virtual int calc_forces(std::vector<colvarvalue> const &values =
-                          std::vector<colvarvalue>(0));
 
   virtual std::string const get_state_params() const;
   virtual int set_state_params(std::string const &state_conf);
@@ -125,7 +124,7 @@ protected:
   virtual void calc_hills(hill_iter  h_first,
                           hill_iter  h_last,
                           cvm::real &energy,
-                          std::vector<colvarvalue> const &values = std::vector<colvarvalue>(0));
+                          std::vector<colvarvalue> const *values);
 
   /// \brief Calculate the forces acting on the i-th colvar,
   /// incrementing colvar_forces[i]; must be called after calc_hills
@@ -134,7 +133,7 @@ protected:
                                 hill_iter h_first,
                                 hill_iter h_last,
                                 std::vector<colvarvalue> &forces,
-                                std::vector<colvarvalue> const &values = std::vector<colvarvalue>(0));
+                                std::vector<colvarvalue> const *values);
 
 
   /// Height of new hills

lib/colvars/colvarbias_restraint.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -174,7 +174,7 @@ int colvarbias_restraint_k::change_configuration(std::string const &conf)
 
 
 
-colvarbias_restraint_moving::colvarbias_restraint_moving(char const *key)
+colvarbias_restraint_moving::colvarbias_restraint_moving(char const * /* key */)
 {
   target_nstages = 0;
   target_nsteps = 0L;

lib/colvars/colvarbias_restraint.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -26,10 +26,10 @@ public:
   virtual int update();
 
   /// Load new configuration - force constant and/or centers only
-  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+  virtual int change_configuration(std::string const & /* conf */) { return COLVARS_NOT_IMPLEMENTED; }
 
   /// Calculate change in energy from using alternate configuration
-  virtual cvm::real energy_difference(std::string const &conf) { return 0.0; }
+  virtual cvm::real energy_difference(std::string const & /* conf */) { return 0.0; }
 
   virtual std::string const get_state_params() const;
   virtual int set_state_params(std::string const &conf);
@@ -107,7 +107,7 @@ public:
   // Note: despite the diamond inheritance, most of this function gets only executed once
   virtual int init(std::string const &conf);
   virtual int update() { return COLVARS_OK; }
-  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+  virtual int change_configuration(std::string const & /* conf */) { return COLVARS_NOT_IMPLEMENTED; }
 
   virtual std::string const get_state_params() const;
   virtual int set_state_params(std::string const &conf);
@@ -149,7 +149,7 @@ public:
   colvarbias_restraint_centers_moving(char const *key);
   virtual int init(std::string const &conf);
   virtual int update();
-  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+  virtual int change_configuration(std::string const & /* conf */) { return COLVARS_NOT_IMPLEMENTED; }
 
   virtual std::string const get_state_params() const;
   virtual int set_state_params(std::string const &conf);
@@ -188,7 +188,7 @@ public:
   colvarbias_restraint_k_moving(char const *key);
   virtual int init(std::string const &conf);
   virtual int update();
-  virtual int change_configuration(std::string const &conf) { return COLVARS_NOT_IMPLEMENTED; }
+  virtual int change_configuration(std::string const & /* conf */) { return COLVARS_NOT_IMPLEMENTED; }
 
   virtual std::string const get_state_params() const;
   virtual int set_state_params(std::string const &conf);

lib/colvars/colvarcomp.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -17,30 +17,28 @@
 
 
 colvar::cvc::cvc()
-  : sup_coeff(1.0),
-    sup_np(1),
-    b_periodic(false),
-    b_try_scalable(true)
 {
   description = "uninitialized colvar component";
-  init_dependencies();
+  b_try_scalable = true;
   sup_coeff = 1.0;
+  sup_np = 1;
   period = 0.0;
   wrap_center = 0.0;
+  width = 0.0;
+  init_dependencies();
 }
 
 
 colvar::cvc::cvc(std::string const &conf)
-  : sup_coeff(1.0),
-    sup_np(1),
-    b_periodic(false),
-    b_try_scalable(true)
 {
   description = "uninitialized colvar component";
-  init_dependencies();
+  b_try_scalable = true;
   sup_coeff = 1.0;
+  sup_np = 1;
   period = 0.0;
   wrap_center = 0.0;
+  width = 0.0;
+  init_dependencies();
   init(conf);
 }
 
@@ -72,11 +70,17 @@ int colvar::cvc::init(std::string const &conf)
 
   get_keyval(conf, "componentCoeff", sup_coeff, sup_coeff);
   get_keyval(conf, "componentExp", sup_np, sup_np);
+  // TODO these could be condensed into get_keyval()
+  register_param("componentCoeff", reinterpret_cast<void *>(&sup_coeff));
+  register_param("componentExp", reinterpret_cast<void *>(&sup_np));
 
   get_keyval(conf, "period", period, period);
   get_keyval(conf, "wrapAround", wrap_center, wrap_center);
+  // TODO when init() is called after all constructors, check periodic flag
+  register_param("period", reinterpret_cast<void *>(&period));
+  register_param("wrapAround", reinterpret_cast<void *>(&wrap_center));
 
-  get_keyval_feature(dynamic_cast<colvarparse *>(this), conf, "debugGradients",
+  get_keyval_feature(this, conf, "debugGradients",
                      f_cvc_debug_gradient, false, parse_silent);
 
   bool b_no_PBC = !is_enabled(f_cvc_pbc_minimum_image); // Enabled by default
@@ -194,6 +198,14 @@ int colvar::cvc::init_dependencies() {
 
     init_feature(f_cvc_scalar, "scalar", f_type_static);
 
+    init_feature(f_cvc_periodic, "periodic", f_type_static);
+
+    init_feature(f_cvc_width, "defined width", f_type_static);
+
+    init_feature(f_cvc_lower_boundary, "defined lower boundary", f_type_static);
+
+    init_feature(f_cvc_upper_boundary, "defined upper boundary", f_type_static);
+
     init_feature(f_cvc_gradient, "gradient", f_type_dynamic);
 
     init_feature(f_cvc_explicit_gradient, "explicit gradient", f_type_static);
@@ -209,15 +221,15 @@ int colvar::cvc::init_dependencies() {
     init_feature(f_cvc_Jacobian, "Jacobian derivative", f_type_dynamic);
     require_feature_self(f_cvc_Jacobian, f_cvc_inv_gradient);
 
-    init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);
-
-    init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user);
-
     // Compute total force on first site only to avoid unwanted
     // coupling to other colvars (see e.g. Ciccotti et al., 2005)
     init_feature(f_cvc_one_site_total_force, "compute total force from one group", f_type_user);
     require_feature_self(f_cvc_one_site_total_force, f_cvc_com_based);
 
+    init_feature(f_cvc_com_based, "depends on group centers of mass", f_type_static);
+
+    init_feature(f_cvc_pbc_minimum_image, "use minimum-image distances with PBCs", f_type_user);
+
     init_feature(f_cvc_scalable, "scalable calculation", f_type_static);
     require_feature_self(f_cvc_scalable, f_cvc_scalable_com);
 
@@ -291,6 +303,77 @@ colvar::cvc::~cvc()
 }
 
 
+void colvar::cvc::init_as_distance()
+{
+  x.type(colvarvalue::type_scalar);
+  enable(f_cvc_lower_boundary);
+  lower_boundary.type(colvarvalue::type_scalar);
+  lower_boundary.real_value = 0.0;
+  register_param("lowerBoundary", reinterpret_cast<void *>(&lower_boundary));
+}
+
+
+void colvar::cvc::init_as_angle()
+{
+  x.type(colvarvalue::type_scalar);
+  init_scalar_boundaries(0.0, 180);
+}
+
+
+void colvar::cvc::init_scalar_boundaries(cvm::real lb, cvm::real ub)
+{
+  enable(f_cvc_lower_boundary);
+  lower_boundary.type(colvarvalue::type_scalar);
+  lower_boundary.real_value = lb;
+  enable(f_cvc_upper_boundary);
+  upper_boundary.type(colvarvalue::type_scalar);
+  upper_boundary.real_value = ub;
+  register_param("lowerBoundary", reinterpret_cast<void *>(&lower_boundary));
+  register_param("upperBoundary", reinterpret_cast<void *>(&upper_boundary));
+}
+
+
+void colvar::cvc::register_atom_group(cvm::atom_group *ag)
+{
+  atom_groups.push_back(ag);
+  add_child(ag);
+}
+
+
+colvarvalue const *colvar::cvc::get_param_grad(std::string const &param_name)
+{
+  colvarvalue const *ptr =
+    reinterpret_cast<colvarvalue const *>(get_param_grad_ptr(param_name));
+  return ptr != NULL ? ptr : NULL;
+}
+
+
+int colvar::cvc::set_param(std::string const &param_name,
+                           void const *new_value)
+{
+  if (param_map.count(param_name) > 0) {
+
+    // TODO When we can use C++11, make this a proper function map
+    if (param_name.compare("componentCoeff") == 0) {
+      sup_coeff = *(reinterpret_cast<cvm::real const *>(new_value));
+    }
+    if (param_name.compare("componentExp") == 0) {
+      sup_np = *(reinterpret_cast<int const *>(new_value));
+    }
+    if (is_enabled(f_cvc_periodic)) {
+      if (param_name.compare("period") == 0) {
+        period = *(reinterpret_cast<cvm::real const *>(new_value));
+      }
+      if (param_name.compare("wrapAround") == 0) {
+        wrap_center = *(reinterpret_cast<cvm::real const *>(new_value));
+      }
+    }
+  }
+
+  return colvarparams::set_param(param_name, new_value);
+}
+
+
 void colvar::cvc::read_data()
 {
   size_t ig;
@@ -537,7 +620,7 @@ colvarvalue colvar::cvc::dist2_rgrad(colvarvalue const &x1,
 }
 
 
-void colvar::cvc::wrap(colvarvalue &x_unwrapped) const
+void colvar::cvc::wrap(colvarvalue & /* x_unwrapped */) const
 {
   return;
 }

lib/colvars/colvarcomp.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -23,11 +23,13 @@
 #include "colvarmodule.h"
 #include "colvar.h"
 #include "colvaratoms.h"
+#include "colvar_arithmeticpath.h"
 
 #if (__cplusplus >= 201103L)
+// C++11-only functions
 #include "colvar_geometricpath.h"
 #include <functional>
-#endif // C++11 checking
+#endif
 
 #include <map>
 
@@ -97,10 +99,7 @@ public:
   /// \brief Exponent in the polynomial combination (default: 1)
   int       sup_np;
 
-  /// \brief Is this a periodic component?
+  /// \brief Period of the values of this CVC (default: 0.0, non periodic)
-  bool b_periodic;
-
-  /// \brief Period of this cvc value, (default: 0.0, non periodic)
   cvm::real period;
 
   /// \brief If the component is periodic, wrap around this value (default: 0.0)
@@ -261,10 +260,13 @@ public:
   std::vector<cvm::atom_group *> atom_groups;
 
   /// \brief Store a pointer to new atom group, and list as child for dependencies
-  inline void register_atom_group(cvm::atom_group *ag) {
+  void register_atom_group(cvm::atom_group *ag);
-    atom_groups.push_back(ag);
+
-    add_child(ag);
+  /// Pointer to the gradient of parameter param_name
-  }
+  virtual colvarvalue const *get_param_grad(std::string const &param_name);
+
+  /// Set the named parameter to the given value
+  virtual int set_param(std::string const &param_name, void const *new_value);
 
   /// \brief Whether or not this CVC will be computed in parallel whenever possible
   bool b_try_scalable;
@@ -286,6 +288,24 @@ protected:
   /// \brief Calculated Jacobian derivative (divergence of the inverse
   /// gradients): serves to calculate the phase space correction
   colvarvalue jd;
+
+  /// \brief Set data types for a scalar distance (convenience function)
+  void init_as_distance();
+
+  /// \brief Set data types for a bounded angle (convenience function)
+  void init_as_angle();
+
+  /// \brief Set two scalar boundaries (convenience function)
+  void init_scalar_boundaries(cvm::real lb, cvm::real ub);
+
+  /// \brief Location of the lower boundary (not defined by user choice)
+  colvarvalue lower_boundary;
+
+  /// \brief Location of the upper boundary (not defined by user choice)
+  colvarvalue upper_boundary;
+
+  /// \brief CVC-specific default colvar width
+  cvm::real width;
 };
 
 
@@ -538,7 +558,6 @@ protected:
   bool b_no_PBC;
 public:
   distance_inv(std::string const &conf);
-  distance_inv();
   virtual ~distance_inv() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -614,9 +633,7 @@ protected:
   /// Atoms involved
   cvm::atom_group  *atoms;
 public:
-  /// Constructor
   gyration(std::string const &conf);
-  gyration();
   virtual ~gyration() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -752,7 +769,6 @@ public:
   angle(std::string const &conf);
   /// \brief Initialize the three groups after three atoms
   angle(cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3);
-  angle();
   virtual ~angle() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -902,7 +918,6 @@ protected:
 public:
 
   coordnum(std::string const &conf);
-  coordnum();
   ~coordnum();
 
   virtual void calc_value();
@@ -972,7 +987,6 @@ protected:
 public:
 
   selfcoordnum(std::string const &conf);
-  selfcoordnum();
   ~selfcoordnum();
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1011,7 +1025,6 @@ protected:
 public:
   /// Constructor
   groupcoordnum(std::string const &conf);
-  groupcoordnum();
   virtual ~groupcoordnum() {}
   virtual void calc_value();
   virtual void calc_gradients();
@@ -1232,7 +1245,6 @@ class colvar::orientation_angle
 public:
 
   orientation_angle(std::string const &conf);
-  orientation_angle();
   virtual int init(std::string const &conf);
   virtual ~orientation_angle() {}
   virtual void calc_value();
@@ -1285,7 +1297,6 @@ protected:
 public:
 
   tilt(std::string const &conf);
-  tilt();
   virtual int init(std::string const &conf);
   virtual ~tilt() {}
   virtual void calc_value();
@@ -1394,13 +1405,13 @@ class colvar::componentDisabled
   : public colvar::cvc
 {
 public:
-    componentDisabled(std::string const &conf) {
+    componentDisabled(std::string const & /* conf */) {
         cvm::error("Error: this component is not enabled in the current build; please see https://colvars.github.io/README-c++11.html");
     }
     virtual ~componentDisabled() {}
     virtual void calc_value() {}
     virtual void calc_gradients() {}
-    virtual void apply_force(colvarvalue const &force) {}
+    virtual void apply_force(colvarvalue const & /* force */) {}
 };
 
 
@@ -1410,7 +1421,7 @@ class colvar::CartesianBasedPath
   : public colvar::cvc
 {
 protected:
-    virtual void computeReferenceDistance(std::vector<cvm::real>& result);
+    virtual void computeDistanceToReferenceFrames(std::vector<cvm::real>& result);
     /// Selected atoms
     cvm::atom_group *atoms;
     /// Fitting options
@@ -1440,7 +1451,7 @@ private:
     cvm::rotation rot_v3;
 protected:
     virtual void prepareVectors();
-    virtual void updateReferenceDistances();
+    virtual void updateDistanceToReferenceFrames();
 public:
     gspath(std::string const &conf);
     virtual ~gspath() {}
@@ -1462,7 +1473,7 @@ private:
     cvm::rotation rot_v4;
 protected:
     virtual void prepareVectors();
-    virtual void updateReferenceDistances();
+    virtual void updateDistanceToReferenceFrames();
 public:
     gzpath(std::string const &conf);
     virtual ~gzpath() {}
@@ -1508,7 +1519,9 @@ protected:
     /// Total number of reference frames
     size_t total_reference_frames;
 protected:
-    virtual void computeReferenceDistance(std::vector<cvm::real>& result);
+    virtual void computeDistanceToReferenceFrames(std::vector<cvm::real>& result);
+    /// Helper function to determine the distance between reference frames
+    virtual void computeDistanceBetweenReferenceFrames(std::vector<cvm::real>& result) const;
     cvm::real getPolynomialFactorOfCVGradient(size_t i_cv) const;
 public:
     CVBasedPath(std::string const &conf);
@@ -1526,7 +1539,7 @@ class colvar::gspathCV
   : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>
 {
 protected:
-    virtual void updateReferenceDistances();
+    virtual void updateDistanceToReferenceFrames();
     virtual void prepareVectors();
 public:
     gspathCV(std::string const &conf);
@@ -1542,7 +1555,7 @@ class colvar::gzpathCV
   : public colvar::CVBasedPath, public GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>
 {
 protected:
-    virtual void updateReferenceDistances();
+    virtual void updateDistanceToReferenceFrames();
     virtual void prepareVectors();
 public:
     gzpathCV(std::string const &conf);
@@ -1552,6 +1565,35 @@ public:
     virtual void apply_force(colvarvalue const &force);
 };
 
+
+
+class colvar::aspathCV
+  : public colvar::CVBasedPath, public ArithmeticPathCV::ArithmeticPathBase<colvarvalue, cvm::real, ArithmeticPathCV::path_sz::S>
+{
+protected:
+    virtual void updateDistanceToReferenceFrames();
+public:
+    aspathCV(std::string const &conf);
+    virtual ~aspathCV();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
+
+class colvar::azpathCV
+  : public colvar::CVBasedPath, public ArithmeticPathCV::ArithmeticPathBase<colvarvalue, cvm::real, ArithmeticPathCV::path_sz::Z>
+{
+protected:
+    virtual void updateDistanceToReferenceFrames();
+public:
+    azpathCV(std::string const &conf);
+    virtual ~azpathCV();
+    virtual void calc_value();
+    virtual void calc_gradients();
+    virtual void apply_force(colvarvalue const &force);
+};
+
 #else // if the compiler doesn't support C++11
 
 class colvar::linearCombination
@@ -1603,6 +1645,20 @@ public:
     gzpathCV(std::string const &conf) : componentDisabled(conf) {}
 };
 
+class colvar::aspathCV
+  : public colvar::componentDisabled
+{
+public:
+    aspathCV(std::string const &conf) : componentDisabled(conf) {}
+};
+
+class colvar::azpathCV
+  : public colvar::componentDisabled
+{
+public:
+    azpathCV(std::string const &conf) : componentDisabled(conf) {}
+};
+
 #endif // C++11 checking
 
 // metrics functions for cvc implementations

lib/colvars/colvarcomp_angles.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -16,6 +16,8 @@ colvar::angle::angle(std::string const &conf)
   : cvc(conf)
 {
   function_type = "angle";
+  init_as_angle();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
@@ -25,8 +27,6 @@ colvar::angle::angle(std::string const &conf)
   group3 = parse_group(conf, "group3");
 
   init_total_force_params(conf);
-
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -35,6 +35,8 @@ colvar::angle::angle(cvm::atom const &a1,
                      cvm::atom const &a3)
 {
   function_type = "angle";
+  init_as_angle();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
@@ -45,15 +47,6 @@ colvar::angle::angle(cvm::atom const &a1,
   register_atom_group(group1);
   register_atom_group(group2);
   register_atom_group(group3);
-
-  x.type(colvarvalue::type_scalar);
-}
-
-
-colvar::angle::angle()
-{
-  function_type = "angle";
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -148,13 +141,13 @@ colvar::dipole_angle::dipole_angle(std::string const &conf)
   : cvc(conf)
 {
   function_type = "dipole_angle";
+  init_as_angle();
+
   group1 = parse_group(conf, "group1");
   group2 = parse_group(conf, "group2");
   group3 = parse_group(conf, "group3");
 
   init_total_force_params(conf);
-
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -178,6 +171,7 @@ colvar::dipole_angle::dipole_angle(cvm::atom const &a1,
 colvar::dipole_angle::dipole_angle()
 {
   function_type = "dipole_angle";
+  init_as_angle();
   x.type(colvarvalue::type_scalar);
 }
 
@@ -259,7 +253,7 @@ colvar::dihedral::dihedral(std::string const &conf)
 {
   function_type = "dihedral";
   period = 360.0;
-  b_periodic = true;
+  enable(f_cvc_periodic);
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
@@ -285,7 +279,7 @@ colvar::dihedral::dihedral(cvm::atom const &a1,
 
   function_type = "dihedral";
   period = 360.0;
-  b_periodic = true;
+  enable(f_cvc_periodic);
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
@@ -312,7 +306,7 @@ colvar::dihedral::dihedral()
 {
   function_type = "dihedral";
   period = 360.0;
-  b_periodic = true;
+  enable(f_cvc_periodic);
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   x.type(colvarvalue::type_scalar);

lib/colvars/colvarcomp_apath.cpp

@@ -0,0 +1,192 @@
+#if (__cplusplus >= 201103L)
+
+#include <numeric>
+#include <algorithm>
+#include <cmath>
+#include <cstdlib>
+#include <limits>
+
+#include "colvarmodule.h"
+#include "colvarvalue.h"
+#include "colvarparse.h"
+#include "colvar.h"
+#include "colvarcomp.h"
+
+colvar::aspathCV::aspathCV(std::string const &conf): CVBasedPath(conf) {
+    function_type = "aspathCV";
+    cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
+    std::vector<cvm::real> p_weights(cv.size(), 1.0);
+    get_keyval(conf, "weights", p_weights, std::vector<cvm::real>(cv.size(), 1.0));
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    std::vector<cvm::real> rmsd_between_refs(total_reference_frames - 1, 0.0);
+    computeDistanceBetweenReferenceFrames(rmsd_between_refs);
+    cvm::real mean_square_displacements = 0.0;
+    for (size_t i_frame = 1; i_frame < total_reference_frames; ++i_frame) {
+        cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n"));
+        mean_square_displacements += rmsd_between_refs[i_frame - 1] * rmsd_between_refs[i_frame - 1];
+    }
+    mean_square_displacements /= cvm::real(total_reference_frames - 1);
+    cvm::real suggested_lambda = 1.0 / mean_square_displacements;
+    cvm::real p_lambda;
+    get_keyval(conf, "lambda", p_lambda, suggested_lambda);
+    ArithmeticPathCV::ArithmeticPathBase<colvarvalue, cvm::real, ArithmeticPathCV::path_sz::S>::initialize(cv.size(), total_reference_frames, p_lambda, ref_cv[0], p_weights);
+    cvm::log(std::string("Lambda is ") + cvm::to_str(lambda) + std::string("\n"));
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+        cvm::log(std::string("The weight of CV ") + cvm::to_str(i_cv) + std::string(" is ") + cvm::to_str(weights[i_cv]) + std::string("\n"));
+    }
+}
+
+void colvar::aspathCV::updateDistanceToReferenceFrames() {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_value();
+    }
+    for (size_t i_frame = 0; i_frame < ref_cv.size(); ++i_frame) {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]);
+            colvarvalue current_cv_value(cv[i_cv]->value());
+            if (current_cv_value.type() == colvarvalue::type_scalar) {
+                frame_element_distances[i_frame][i_cv] = 0.5 * cv[i_cv]->dist2_lgrad(cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)), ref_cv_value.real_value);
+            } else {
+                frame_element_distances[i_frame][i_cv] = 0.5 * cv[i_cv]->dist2_lgrad(cv[i_cv]->sup_coeff * current_cv_value, ref_cv_value);
+            }
+        }
+    }
+}
+
+void colvar::aspathCV::calc_value() {
+    computeValue();
+    x = s;
+}
+
+void colvar::aspathCV::calc_gradients() {
+    computeDerivatives();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_gradients();
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = dsdx[i_cv][j_elem] * factor_polynomial * (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad;
+                    }
+                }
+            }
+        }
+    }
+}
+
+void colvar::aspathCV::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)
+        ) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        } else {
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            colvarvalue cv_force = dsdx[i_cv] * force.real_value * factor_polynomial;
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+colvar::aspathCV::~aspathCV() {}
+
+colvar::azpathCV::azpathCV(std::string const &conf): CVBasedPath(conf) {
+    function_type = "azpathCV";
+    cvm::log(std::string("Total number of frames: ") + cvm::to_str(total_reference_frames) + std::string("\n"));
+    std::vector<cvm::real> p_weights(cv.size(), 1.0);
+    get_keyval(conf, "weights", p_weights, std::vector<cvm::real>(cv.size(), 1.0));
+    x.type(colvarvalue::type_scalar);
+    use_explicit_gradients = true;
+    std::vector<cvm::real> rmsd_between_refs(total_reference_frames - 1, 0.0);
+    computeDistanceBetweenReferenceFrames(rmsd_between_refs);
+    cvm::real mean_square_displacements = 0.0;
+    for (size_t i_frame = 1; i_frame < total_reference_frames; ++i_frame) {
+        cvm::log(std::string("Distance between frame ") + cvm::to_str(i_frame) + " and " + cvm::to_str(i_frame + 1) + " is " + cvm::to_str(rmsd_between_refs[i_frame - 1]) + std::string("\n"));
+        mean_square_displacements += rmsd_between_refs[i_frame - 1] * rmsd_between_refs[i_frame - 1];
+    }
+    mean_square_displacements /= cvm::real(total_reference_frames - 1);
+    cvm::real suggested_lambda = 1.0 / mean_square_displacements;
+    cvm::real p_lambda;
+    get_keyval(conf, "lambda", p_lambda, suggested_lambda);
+    ArithmeticPathCV::ArithmeticPathBase<colvarvalue, cvm::real, ArithmeticPathCV::path_sz::Z>::initialize(cv.size(), total_reference_frames, p_lambda, ref_cv[0], p_weights);
+    cvm::log(std::string("Lambda is ") + cvm::to_str(lambda) + std::string("\n"));
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if (!cv[i_cv]->is_enabled(f_cvc_explicit_gradient)) {
+            use_explicit_gradients = false;
+        }
+        cvm::log(std::string("The weight of CV ") + cvm::to_str(i_cv) + std::string(" is ") + cvm::to_str(weights[i_cv]) + std::string("\n"));
+    }
+}
+
+void colvar::azpathCV::updateDistanceToReferenceFrames() {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_value();
+    }
+    for (size_t i_frame = 0; i_frame < ref_cv.size(); ++i_frame) {
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]);
+            colvarvalue current_cv_value(cv[i_cv]->value());
+            if (current_cv_value.type() == colvarvalue::type_scalar) {
+                frame_element_distances[i_frame][i_cv] = 0.5 * cv[i_cv]->dist2_lgrad(cv[i_cv]->sup_coeff * (cvm::pow(current_cv_value.real_value, cv[i_cv]->sup_np)), ref_cv_value.real_value);
+            } else {
+                frame_element_distances[i_frame][i_cv] = 0.5 * cv[i_cv]->dist2_lgrad(cv[i_cv]->sup_coeff * current_cv_value, ref_cv_value);
+            }
+        }
+    }
+}
+
+void colvar::azpathCV::calc_value() {
+    computeValue();
+    x = z;
+}
+
+void colvar::azpathCV::calc_gradients() {
+    computeDerivatives();
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        cv[i_cv]->calc_gradients();
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)) {
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            for (size_t j_elem = 0; j_elem < cv[i_cv]->value().size(); ++j_elem) {
+                for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                    for (size_t l_atom = 0; l_atom < (cv[i_cv]->atom_groups)[k_ag]->size(); ++l_atom) {
+                        (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad = dzdx[i_cv][j_elem] * factor_polynomial * (*(cv[i_cv]->atom_groups)[k_ag])[l_atom].grad;
+                    }
+                }
+            }
+
+        }
+    }
+}
+
+void colvar::azpathCV::apply_force(colvarvalue const &force) {
+    for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+        if ( cv[i_cv]->is_enabled(f_cvc_explicit_gradient) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable) &&
+            !cv[i_cv]->is_enabled(f_cvc_scalable_com)
+        ) {
+            for (size_t k_ag = 0 ; k_ag < cv[i_cv]->atom_groups.size(); ++k_ag) {
+                (cv[i_cv]->atom_groups)[k_ag]->apply_colvar_force(force.real_value);
+            }
+        } else {
+            cvm::real factor_polynomial = getPolynomialFactorOfCVGradient(i_cv);
+            const colvarvalue cv_force = dzdx[i_cv] * force.real_value * factor_polynomial;
+            cv[i_cv]->apply_force(cv_force);
+        }
+    }
+}
+
+colvar::azpathCV::~azpathCV() {}
+
+#endif

lib/colvars/colvarcomp_coordnums.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -97,6 +97,8 @@ colvar::coordnum::coordnum(std::string const &conf)
   function_type = "coordnum";
   x.type(colvarvalue::type_scalar);
 
+  colvarproxy *proxy = cvm::main()->proxy;
+
   group1 = parse_group(conf, "group1");
   group2 = parse_group(conf, "group2");
 
@@ -119,12 +121,12 @@ colvar::coordnum::coordnum(std::string const &conf)
   }
 
   bool const b_isotropic = get_keyval(conf, "cutoff", r0,
-                                      cvm::real(4.0 * cvm::unit_angstrom()));
+                                      cvm::real(4.0 * proxy->angstrom_value));
 
   if (get_keyval(conf, "cutoff3", r0_vec,
-                 cvm::rvector(4.0 * cvm::unit_angstrom(),
+                 cvm::rvector(4.0 * proxy->angstrom_value,
-                              4.0 * cvm::unit_angstrom(),
+                              4.0 * proxy->angstrom_value,
-                              4.0 * cvm::unit_angstrom()))) {
+                              4.0 * proxy->angstrom_value))) {
     if (b_isotropic) {
       cvm::error("Error: cannot specify \"cutoff\" and \"cutoff3\" "
                  "at the same time.\n",
@@ -174,14 +176,8 @@ colvar::coordnum::coordnum(std::string const &conf)
     }
   }
 
-}
+  init_scalar_boundaries(0.0, b_group2_center_only ? group1->size() :
-
+                         group1->size() * group2->size());
-
-colvar::coordnum::coordnum()
-  : b_anisotropic(false), pairlist(NULL)
-{
-  function_type = "coordnum";
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -310,10 +306,13 @@ colvar::h_bond::h_bond(std::string const &conf)
 
   function_type = "h_bond";
   x.type(colvarvalue::type_scalar);
+  init_scalar_boundaries(0.0, 1.0);
 
-  int a_num, d_num;
+  colvarproxy *proxy = cvm::main()->proxy;
-  get_keyval(conf, "acceptor", a_num, -1);
+
-  get_keyval(conf, "donor",    d_num, -1);
+  int a_num = -1, d_num = -1;
+  get_keyval(conf, "acceptor", a_num, a_num);
+  get_keyval(conf, "donor",    d_num, a_num);
 
   if ( (a_num == -1) || (d_num == -1) ) {
     cvm::error("Error: either acceptor or donor undefined.\n");
@@ -326,7 +325,7 @@ colvar::h_bond::h_bond(std::string const &conf)
   atom_groups[0]->add_atom(acceptor);
   atom_groups[0]->add_atom(donor);
 
-  get_keyval(conf, "cutoff",   r0, (3.3 * cvm::unit_angstrom()));
+  get_keyval(conf, "cutoff",   r0, (3.3 * proxy->angstrom_value));
   get_keyval(conf, "expNumer", en, 6);
   get_keyval(conf, "expDenom", ed, 8);
 
@@ -352,6 +351,7 @@ colvar::h_bond::h_bond(cvm::atom const &acceptor,
 {
   function_type = "h_bond";
   x.type(colvarvalue::type_scalar);
+  init_scalar_boundaries(0.0, 1.0);
 
   register_atom_group(new cvm::atom_group);
   atom_groups[0]->add_atom(acceptor);
@@ -359,14 +359,6 @@ colvar::h_bond::h_bond(cvm::atom const &acceptor,
 }
 
 
-colvar::h_bond::h_bond()
-  : cvc()
-{
-  function_type = "h_bond";
-  x.type(colvarvalue::type_scalar);
-}
-
-
 void colvar::h_bond::calc_value()
 {
   int const flags = coordnum::ef_null;
@@ -406,9 +398,11 @@ colvar::selfcoordnum::selfcoordnum(std::string const &conf)
   function_type = "selfcoordnum";
   x.type(colvarvalue::type_scalar);
 
+  colvarproxy *proxy = cvm::main()->proxy;
+
   group1 = parse_group(conf, "group1");
 
-  get_keyval(conf, "cutoff", r0, cvm::real(4.0 * cvm::unit_angstrom()));
+  get_keyval(conf, "cutoff", r0, cvm::real(4.0 * proxy->angstrom_value));
   get_keyval(conf, "expNumer", en, 6);
   get_keyval(conf, "expDenom", ed, 12);
 
@@ -437,14 +431,8 @@ colvar::selfcoordnum::selfcoordnum(std::string const &conf)
     }
     pairlist = new bool[(group1->size()-1) * (group1->size()-1)];
   }
-}
 
-
+  init_scalar_boundaries(0.0, (group1->size()-1) * (group1->size()-1));
-colvar::selfcoordnum::selfcoordnum()
-  : pairlist(NULL)
-{
-  function_type = "selfcoordnum";
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -553,6 +541,9 @@ colvar::groupcoordnum::groupcoordnum(std::string const &conf)
 {
   function_type = "groupcoordnum";
   x.type(colvarvalue::type_scalar);
+  init_scalar_boundaries(0.0, 1.0);
+
+  colvarproxy *proxy = cvm::main()->proxy;
 
   // group1 and group2 are already initialized by distance()
   if (group1->b_dummy || group2->b_dummy) {
@@ -561,7 +552,7 @@ colvar::groupcoordnum::groupcoordnum(std::string const &conf)
   }
 
   bool const b_scale = get_keyval(conf, "cutoff", r0,
-                                  cvm::real(4.0 * cvm::unit_angstrom()));
+                                  cvm::real(4.0 * proxy->angstrom_value));
 
   if (get_keyval(conf, "cutoff3", r0_vec,
                  cvm::rvector(4.0, 4.0, 4.0), parse_silent)) {
@@ -598,14 +589,6 @@ colvar::groupcoordnum::groupcoordnum(std::string const &conf)
 }
 
 
-colvar::groupcoordnum::groupcoordnum()
-  : b_anisotropic(false)
-{
-  function_type = "groupcoordnum";
-  x.type(colvarvalue::type_scalar);
-}
-
-
 void colvar::groupcoordnum::calc_value()
 {
   // create fake atoms to hold the com coordinates

lib/colvars/colvarcomp_distances.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -19,6 +19,8 @@ colvar::distance::distance(std::string const &conf)
   : cvc(conf)
 {
   function_type = "distance";
+  init_as_distance();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
@@ -27,8 +29,6 @@ colvar::distance::distance(std::string const &conf)
   group2 = parse_group(conf, "group2");
 
   init_total_force_params(conf);
-
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -36,10 +36,11 @@ colvar::distance::distance()
   : cvc()
 {
   function_type = "distance";
+  init_as_distance();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -177,7 +178,7 @@ colvar::distance_z::distance_z(std::string const &conf)
   // TODO detect PBC from MD engine (in simple cases)
   // and then update period in real time
   if (period != 0.0)
-    b_periodic = true;
+    enable(f_cvc_periodic);
 
   if ((wrap_center != 0.0) && (period == 0.0)) {
     cvm::error("Error: wrapAround was defined in a distanceZ component,"
@@ -317,7 +318,7 @@ cvm::real colvar::distance_z::dist2(colvarvalue const &x1,
                                     colvarvalue const &x2) const
 {
   cvm::real diff = x1.real_value - x2.real_value;
-  if (b_periodic) {
+  if (is_enabled(f_cvc_periodic)) {
     cvm::real shift = cvm::floor(diff/period + 0.5);
     diff -= shift * period;
   }
@@ -329,7 +330,7 @@ colvarvalue colvar::distance_z::dist2_lgrad(colvarvalue const &x1,
                                             colvarvalue const &x2) const
 {
   cvm::real diff = x1.real_value - x2.real_value;
-  if (b_periodic) {
+  if (is_enabled(f_cvc_periodic)) {
     cvm::real shift = cvm::floor(diff/period + 0.5);
     diff -= shift * period;
   }
@@ -341,7 +342,7 @@ colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1,
                                             colvarvalue const &x2) const
 {
   cvm::real diff = x1.real_value - x2.real_value;
-  if (b_periodic) {
+  if (is_enabled(f_cvc_periodic)) {
     cvm::real shift = cvm::floor(diff/period + 0.5);
     diff -= shift * period;
   }
@@ -351,15 +352,13 @@ colvarvalue colvar::distance_z::dist2_rgrad(colvarvalue const &x1,
 
 void colvar::distance_z::wrap(colvarvalue &x_unwrapped) const
 {
-  if (!b_periodic) {
+  if (!is_enabled(f_cvc_periodic)) {
     // don't wrap if the period has not been set
     return;
   }
-
   cvm::real shift =
     cvm::floor((x_unwrapped.real_value - wrap_center) / period + 0.5);
   x_unwrapped.real_value -= shift * period;
-  return;
 }
 
 
@@ -368,10 +367,11 @@ colvar::distance_xy::distance_xy(std::string const &conf)
   : distance_z(conf)
 {
   function_type = "distance_xy";
+  init_as_distance();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -379,10 +379,11 @@ colvar::distance_xy::distance_xy()
   : distance_z()
 {
   function_type = "distance_xy";
+  init_as_distance();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   enable(f_cvc_com_based);
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -557,6 +558,7 @@ colvar::distance_inv::distance_inv(std::string const &conf)
   : cvc(conf)
 {
   function_type = "distance_inv";
+  init_as_distance();
 
   group1 = parse_group(conf, "group1");
   group2 = parse_group(conf, "group2");
@@ -585,16 +587,6 @@ colvar::distance_inv::distance_inv(std::string const &conf)
              "for distanceInv, because its value and gradients are computed "
              "simultaneously.\n");
   }
-
-  x.type(colvarvalue::type_scalar);
-}
-
-
-colvar::distance_inv::distance_inv()
-{
-  function_type = "distance_inv";
-  exponent = 6;
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -807,6 +799,8 @@ colvar::gyration::gyration(std::string const &conf)
   : cvc(conf)
 {
   function_type = "gyration";
+  init_as_distance();
+
   provide(f_cvc_inv_gradient);
   provide(f_cvc_Jacobian);
   atoms = parse_group(conf, "atoms");
@@ -818,17 +812,6 @@ colvar::gyration::gyration(std::string const &conf)
     atoms->ref_pos.assign(1, cvm::atom_pos(0.0, 0.0, 0.0));
     atoms->fit_gradients.assign(atoms->size(), cvm::rvector(0.0, 0.0, 0.0));
   }
-
-  x.type(colvarvalue::type_scalar);
-}
-
-
-colvar::gyration::gyration()
-{
-  function_type = "gyration";
-  provide(f_cvc_inv_gradient);
-  provide(f_cvc_Jacobian);
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -885,14 +868,7 @@ colvar::inertia::inertia(std::string const &conf)
   : gyration(conf)
 {
   function_type = "inertia";
-  x.type(colvarvalue::type_scalar);
+  init_as_distance();
-}
-
-
-colvar::inertia::inertia()
-{
-  function_type = "inertia";
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -928,9 +904,10 @@ colvar::inertia_z::inertia_z(std::string const &conf)
   : inertia(conf)
 {
   function_type = "inertia_z";
+  init_as_distance();
   if (get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0))) {
     if (axis.norm2() == 0.0) {
-      cvm::error("Axis vector is zero!");
+      cvm::error("Axis vector is zero!", INPUT_ERROR);
       return;
     }
     if (axis.norm2() != 1.0) {
@@ -938,14 +915,6 @@ colvar::inertia_z::inertia_z(std::string const &conf)
       cvm::log("The normalized axis is: "+cvm::to_str(axis)+".\n");
     }
   }
-  x.type(colvarvalue::type_scalar);
-}
-
-
-colvar::inertia_z::inertia_z()
-{
-  function_type = "inertia_z";
-  x.type(colvarvalue::type_scalar);
 }
 
 
@@ -982,9 +951,10 @@ simple_scalar_dist_functions(inertia)
 colvar::rmsd::rmsd(std::string const &conf)
   : cvc(conf)
 {
-  provide(f_cvc_inv_gradient);
   function_type = "rmsd";
-  x.type(colvarvalue::type_scalar);
+  init_as_distance();
+
+  provide(f_cvc_inv_gradient);
 
   atoms = parse_group(conf, "atoms");
 

lib/colvars/colvarcomp_gpath.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -119,9 +119,10 @@ colvar::CartesianBasedPath::~CartesianBasedPath() {
             (*it_comp_atoms) = nullptr;
         }
     }
+    atom_groups.clear();
 }
 
-void colvar::CartesianBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
+void colvar::CartesianBasedPath::computeDistanceToReferenceFrames(std::vector<cvm::real>& result) {
     for (size_t i_frame = 0; i_frame < reference_frames.size(); ++i_frame) {
         cvm::real frame_rmsd = 0.0;
         for (size_t i_atom = 0; i_atom < atoms->size(); ++i_atom) {
@@ -147,13 +148,16 @@ colvar::gspath::gspath(std::string const &conf): CartesianBasedPath(conf) {
     } else {
         cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
     }
+    if (total_reference_frames < 2) {
+        cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) + " reference frames, but gspath requires at least 2 frames.\n");
+    }
     GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::S>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame);
     cvm::log(std::string("Geometric pathCV(s) is initialized.\n"));
     cvm::log(std::string("Geometric pathCV(s) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
 }
 
-void colvar::gspath::updateReferenceDistances() {
+void colvar::gspath::updateDistanceToReferenceFrames() {
-    computeReferenceDistance(frame_distances);
+    computeDistanceToReferenceFrames(frame_distances);
 }
 
 void colvar::gspath::prepareVectors() {
@@ -290,14 +294,17 @@ colvar::gzpath::gzpath(std::string const &conf): CartesianBasedPath(conf) {
     if (b_use_z_square == true) {
         cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
     }
+    if (total_reference_frames < 2) {
+        cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) + " reference frames, but gzpath requires at least 2 frames.\n");
+    }
     GeometricPathCV::GeometricPathBase<cvm::atom_pos, cvm::real, GeometricPathCV::path_sz::Z>::initialize(atoms->size(), cvm::atom_pos(), total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
     // Logging
     cvm::log(std::string("Geometric pathCV(z) is initialized.\n"));
     cvm::log(std::string("Geometric pathCV(z) loaded ") + cvm::to_str(reference_frames.size()) + std::string(" frames.\n"));
 }
 
-void colvar::gzpath::updateReferenceDistances() {
+void colvar::gzpath::updateDistanceToReferenceFrames() {
-    computeReferenceDistance(frame_distances);
+    computeDistanceToReferenceFrames(frame_distances);
 }
 
 void colvar::gzpath::prepareVectors() {
@@ -538,6 +545,7 @@ colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
         std::vector<std::string> fields;
         split_string(line, token, fields);
         size_t num_value_required = 0;
+        cvm::log(std::string("Reading reference frame ") + cvm::to_str(total_reference_frames + 1) + std::string("\n"));
         for (size_t i_cv = 0; i_cv < tmp_cv.size(); ++i_cv) {
             const size_t value_size = tmp_cv[i_cv].size();
             num_value_required += value_size;
@@ -545,10 +553,9 @@ colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
             if (num_value_required <= fields.size()) {
                 size_t start_index = num_value_required - value_size;
                 for (size_t i = start_index; i < num_value_required; ++i) {
-                    tmp_cv[i_cv][i] = std::atof(fields[i].c_str());
+                    tmp_cv[i_cv][i - start_index] = std::atof(fields[i].c_str());
-                    cvm::log(fields[i] + std::string(" "));
+                    cvm::log(cvm::to_str(tmp_cv[i_cv][i - start_index]));
                 }
-                cvm::log(std::string("\n"));
             } else {
                 cvm::error("Error: incorrect format of path file.\n");
             }
@@ -558,6 +565,9 @@ colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
             ++total_reference_frames;
         }
     }
+    if (total_reference_frames <= 1) {
+	cvm::error("Error: there is only 1 or 0 reference frame, which doesn't constitute a path.\n");
+    }
     x.type(colvarvalue::type_scalar);
     use_explicit_gradients = true;
     for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
@@ -570,7 +580,7 @@ colvar::CVBasedPath::CVBasedPath(std::string const &conf): cvc(conf) {
     }
 }
 
-void colvar::CVBasedPath::computeReferenceDistance(std::vector<cvm::real>& result) {
+void colvar::CVBasedPath::computeDistanceToReferenceFrames(std::vector<cvm::real>& result) {
     for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
         cv[i_cv]->calc_value();
     }
@@ -593,6 +603,20 @@ void colvar::CVBasedPath::computeReferenceDistance(std::vector<cvm::real>& resul
     }
 }
 
+void colvar::CVBasedPath::computeDistanceBetweenReferenceFrames(std::vector<cvm::real>& result) const {
+    if (ref_cv.size() < 2) return;
+    for (size_t i_frame = 1; i_frame < ref_cv.size(); ++i_frame) {
+        cvm::real dist_ij = 0.0;
+        for (size_t i_cv = 0; i_cv < cv.size(); ++i_cv) {
+            colvarvalue ref_cv_value(ref_cv[i_frame][i_cv]);
+            colvarvalue prev_ref_cv_value(ref_cv[i_frame-1][i_cv]);
+            dist_ij += cv[i_cv]->dist2(ref_cv_value, prev_ref_cv_value);
+        }
+        dist_ij = cvm::sqrt(dist_ij);
+        result[i_frame-1] = dist_ij;
+    }
+}
+
 cvm::real colvar::CVBasedPath::getPolynomialFactorOfCVGradient(size_t i_cv) const {
     cvm::real factor_polynomial = 1.0;
     if (cv[i_cv]->value().type() == colvarvalue::type_scalar) {
@@ -607,6 +631,7 @@ colvar::CVBasedPath::~CVBasedPath() {
     for (auto it = cv.begin(); it != cv.end(); ++it) {
         delete (*it);
     }
+    atom_groups.clear();
 }
 
 colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) {
@@ -625,6 +650,9 @@ colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) {
     } else {
         cvm::log(std::string("Geometric path s(σ) will use the neighbouring frame to compute s_(m+1)\n"));
     }
+    if (total_reference_frames < 2) {
+        cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) + " reference frames, but gspathCV requires at least 2 frames.\n");
+    }
     GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::S>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame);
     x.type(colvarvalue::type_scalar);
     use_explicit_gradients = true;
@@ -641,8 +669,8 @@ colvar::gspathCV::gspathCV(std::string const &conf): CVBasedPath(conf) {
 
 colvar::gspathCV::~gspathCV() {}
 
-void colvar::gspathCV::updateReferenceDistances() {
+void colvar::gspathCV::updateDistanceToReferenceFrames() {
-    computeReferenceDistance(frame_distances);
+    computeDistanceToReferenceFrames(frame_distances);
 }
 
 void colvar::gspathCV::prepareVectors() {
@@ -766,6 +794,9 @@ colvar::gzpathCV::gzpathCV(std::string const &conf): CVBasedPath(conf) {
     if (b_use_z_square == true) {
         cvm::log(std::string("Geometric path z(σ) will use the square of distance from current frame to path compute z\n"));
     }
+    if (total_reference_frames < 2) {
+        cvm::error("Error: you have specified " + cvm::to_str(total_reference_frames) + " reference frames, but gzpathCV requires at least 2 frames.\n");
+    }
     GeometricPathCV::GeometricPathBase<colvarvalue, cvm::real, GeometricPathCV::path_sz::Z>::initialize(cv.size(), ref_cv[0], total_reference_frames, use_second_closest_frame, use_third_closest_frame, b_use_z_square);
     x.type(colvarvalue::type_scalar);
     use_explicit_gradients = true;
@@ -783,8 +814,8 @@ colvar::gzpathCV::gzpathCV(std::string const &conf): CVBasedPath(conf) {
 colvar::gzpathCV::~gzpathCV() {
 }
 
-void colvar::gzpathCV::updateReferenceDistances() {
+void colvar::gzpathCV::updateDistanceToReferenceFrames() {
-    computeReferenceDistance(frame_distances);
+    computeDistanceToReferenceFrames(frame_distances);
 }
 
 void colvar::gzpathCV::prepareVectors() {

lib/colvars/colvarcomp_protein.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -30,6 +30,8 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
   enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 
+  colvarproxy *proxy = cvm::main()->proxy;
+
   std::string segment_id;
   get_keyval(conf, "psfSegID", segment_id, std::string("MAIN"));
 
@@ -91,7 +93,7 @@ colvar::alpha_angles::alpha_angles(std::string const &conf)
   {
     cvm::real r0;
     size_t en, ed;
-    get_keyval(conf, "hBondCutoff",   r0, (3.3 * cvm::unit_angstrom()));
+    get_keyval(conf, "hBondCutoff",   r0, (3.3 * proxy->angstrom_value));
     get_keyval(conf, "hBondExpNumer", en, 6);
     get_keyval(conf, "hBondExpDenom", ed, 8);
 

lib/colvars/colvarcomp_rotations.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -164,8 +164,8 @@ colvar::orientation_angle::orientation_angle(std::string const &conf)
   : orientation()
 {
   function_type = "orientation_angle";
+  init_as_angle();
   enable(f_cvc_explicit_gradient);
-  x.type(colvarvalue::type_scalar);
   init(conf);
 }
 
@@ -176,15 +176,6 @@ int colvar::orientation_angle::init(std::string const &conf)
 }
 
 
-colvar::orientation_angle::orientation_angle()
-  : orientation()
-{
-  function_type = "orientation_angle";
-  enable(f_cvc_explicit_gradient);
-  x.type(colvarvalue::type_scalar);
-}
-
-
 void colvar::orientation_angle::calc_value()
 {
   atoms_cog = atoms->center_of_geometry();
@@ -231,6 +222,7 @@ colvar::orientation_proj::orientation_proj(std::string const &conf)
   function_type = "orientation_proj";
   enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
+  init_scalar_boundaries(0.0, 1.0);
   init(conf);
 }
 
@@ -241,15 +233,6 @@ int colvar::orientation_proj::init(std::string const &conf)
 }
 
 
-colvar::orientation_proj::orientation_proj()
-  : orientation()
-{
-  function_type = "orientation_proj";
-  enable(f_cvc_explicit_gradient);
-  x.type(colvarvalue::type_scalar);
-}
-
-
 void colvar::orientation_proj::calc_value()
 {
   atoms_cog = atoms->center_of_geometry();
@@ -287,6 +270,7 @@ colvar::tilt::tilt(std::string const &conf)
   function_type = "tilt";
   enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
+  init_scalar_boundaries(-1.0, 1.0);
   init(conf);
 }
 
@@ -307,15 +291,6 @@ int colvar::tilt::init(std::string const &conf)
 }
 
 
-colvar::tilt::tilt()
-  : orientation()
-{
-  function_type = "tilt";
-  enable(f_cvc_explicit_gradient);
-  x.type(colvarvalue::type_scalar);
-}
-
-
 void colvar::tilt::calc_value()
 {
   atoms_cog = atoms->center_of_geometry();
@@ -358,7 +333,7 @@ colvar::spin_angle::spin_angle(std::string const &conf)
 {
   function_type = "spin_angle";
   period = 360.0;
-  b_periodic = true;
+  enable(f_cvc_periodic);
   enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
   init(conf);
@@ -386,7 +361,7 @@ colvar::spin_angle::spin_angle()
 {
   function_type = "spin_angle";
   period = 360.0;
-  b_periodic = true;
+  enable(f_cvc_periodic);
   enable(f_cvc_explicit_gradient);
   x.type(colvarvalue::type_scalar);
 }

lib/colvars/colvardeps.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvardeps.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -219,7 +219,7 @@ public:
   /// Implements possible actions to be carried out
   /// when a given feature is enabled
   /// Base function does nothing, can be overloaded
-  virtual void do_feature_side_effects(int id) {}
+  virtual void do_feature_side_effects(int /* id */) {}
 
   // NOTE that all feature enums should start with f_*_active
   enum features_biases {
@@ -296,6 +296,10 @@ public:
     f_cv_lower_boundary,
     /// \brief An upper boundary is defined
     f_cv_upper_boundary,
+    /// \brief The lower boundary is not defined from user's choice
+    f_cv_hard_lower_boundary,
+    /// \brief The upper boundary is not defined from user's choice
+    f_cv_hard_upper_boundary,
     /// \brief Provide a discretization of the values of the colvar to
     /// be used by the biases or in analysis (needs lower and upper
     /// boundary)
@@ -310,6 +314,8 @@ public:
     f_cv_custom_function,
     /// \brief Colvar is periodic
     f_cv_periodic,
+    /// \brief The colvar has only one component
+    f_cv_single_cvc,
     /// \brief is scalar
     f_cv_scalar,
     f_cv_linear,
@@ -321,20 +327,40 @@ public:
   };
 
   enum features_cvc {
+    /// Computation of this CVC is enabled
     f_cvc_active,
+    /// This CVC computes a scalar value
     f_cvc_scalar,
+    /// Values of this CVC lie in a periodic interval
+    f_cvc_periodic,
+    /// This CVC provides a default value for the colvar's width
+    f_cvc_width,
+    /// This CVC provides a default value for the colvar's lower boundary
+    f_cvc_lower_boundary,
+    /// This CVC provides a default value for the colvar's upper boundary
+    f_cvc_upper_boundary,
+    /// CVC calculates atom gradients
     f_cvc_gradient,
-    /// \brief CVC calculates and stores explicit atom gradients
+    /// CVC calculates and stores explicit atom gradients
     f_cvc_explicit_gradient,
+    /// CVC calculates and stores inverse atom gradients (used for total force)
     f_cvc_inv_gradient,
-    /// \brief If enabled, calc_gradients() will call debug_gradients() for every group needed
+    /// CVC calculates the Jacobian term of the total-force expression
-    f_cvc_debug_gradient,
     f_cvc_Jacobian,
-    f_cvc_pbc_minimum_image,
+    /// The total force for this CVC will be computed from one group only
     f_cvc_one_site_total_force,
+    /// calc_gradients() will call debug_gradients() for every group needed
+    f_cvc_debug_gradient,
+    /// With PBCs, minimum-image convention will be used for distances
+    /// (does not affect the periodicity of CVC values, e.g. angles)
+    f_cvc_pbc_minimum_image,
+    /// This CVC is a function of centers of mass
     f_cvc_com_based,
+    /// This CVC can be computed in parallel
     f_cvc_scalable,
+    /// Centers-of-mass used in this CVC can be computed in parallel
     f_cvc_scalable_com,
+    /// Number of CVC features
     f_cvc_ntot
   };
 

lib/colvars/colvargrid.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvargrid.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -209,7 +209,8 @@ public:
   /// \brief "Almost copy-constructor": only copies configuration
   /// parameters from another grid, but doesn't reallocate stuff;
   /// setup() must be called after that;
-  colvar_grid(colvar_grid<T> const &g) : nd(g.nd),
+  colvar_grid(colvar_grid<T> const &g) : colvarparse(),
+					 nd(g.nd),
                                          nx(g.nx),
                                          mult(g.mult),
                                          data(),
@@ -284,8 +285,8 @@ public:
       }
 
       widths.push_back(cv[i]->width);
-      hard_lower_boundaries.push_back(cv[i]->hard_lower_boundary);
+      hard_lower_boundaries.push_back(cv[i]->is_enabled(colvardeps::f_cv_hard_lower_boundary));
-      hard_upper_boundaries.push_back(cv[i]->hard_upper_boundary);
+      hard_upper_boundaries.push_back(cv[i]->is_enabled(colvardeps::f_cv_hard_upper_boundary));
       periodic.push_back(cv[i]->periodic_boundaries());
 
       // By default, get reported colvar value (for extended Lagrangian colvars)
@@ -415,6 +416,20 @@ public:
     return (int) cvm::floor( (value.real_value - lower_boundaries[i].real_value) / widths[i] );
   }
 
+  /// \brief Report the fraction of bin beyond current_bin_scalar()
+  inline cvm::real current_bin_scalar_fraction(int const i) const
+  {
+    return value_to_bin_scalar_fraction(use_actual_value[i] ? cv[i]->actual_value() : cv[i]->value(), i);
+  }
+
+  /// \brief Use the lower boundary and the width to report the fraction of bin
+  /// beyond value_to_bin_scalar() that the provided value is in
+  inline cvm::real value_to_bin_scalar_fraction(colvarvalue const &value, const int i) const
+  {
+    cvm::real x = (value.real_value - lower_boundaries[i].real_value) / widths[i];
+    return x - cvm::floor(x);
+  }
+
   /// \brief Use the lower boundary and the width to report which bin
   /// the provided value is in and assign first or last bin if out of boundaries
   inline int value_to_bin_scalar_bound(colvarvalue const &value, const int i) const

lib/colvars/colvarmodule.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -32,6 +32,8 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
 
   cv_traj_os = NULL;
 
+  xyz_reader_use_count = 0;
+
   if (proxy == NULL) {
     proxy = proxy_in; // Pointer to the proxy object
     parse = new colvarparse(); // Parsing object for global options
@@ -48,13 +50,21 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in)
   cvm::log("Initializing the collective variables module, version "+
            cvm::to_str(COLVARS_VERSION)+".\n");
   cvm::log("Please cite Fiorin et al, Mol Phys 2013:\n "
-           "http://dx.doi.org/10.1080/00268976.2013.813594\n"
+           "https://dx.doi.org/10.1080/00268976.2013.813594\n"
            "in any publication based on this calculation.\n");
 
   if (proxy->smp_enabled() == COLVARS_OK) {
-    cvm::log("SMP parallelism is available.\n");
+    cvm::log("SMP parallelism is enabled; if needed, use \"smp off\" to override this.\n");
   }
 
+#if (__cplusplus >= 201103L)
+  cvm::log("This version was built with the C++11 standard or higher.");
+#else
+  cvm::log("This version was built without the C++11 standard: some features are disabled.\n"
+    "Please see the following link for details:\n"
+    "https://colvars.github.io/README-c++11.html");
+#endif
+
   // set initial default values
 
   // "it_restart" will be set by the input state file, if any;
@@ -260,6 +270,16 @@ int colvarmodule::parse_global_params(std::string const &conf)
   // TODO document and then echo this keyword
   parse->get_keyval(conf, "logLevel", log_level_, log_level_,
                     colvarparse::parse_silent);
+  {
+    std::string units;
+    if (parse->get_keyval(conf, "units", units)) {
+      units = colvarparse::to_lower_cppstr(units);
+      int error_code = proxy->set_unit_system(units, (colvars.size() != 0));
+      if (error_code != COLVARS_OK) {
+        return error_code;
+      }
+    }
+  }
 
   {
     std::string index_file_name;
@@ -1160,8 +1180,7 @@ int colvarmodule::reset()
   }
   colvars.clear();
 
-  index_groups.clear();
+  reset_index_groups();
-  index_group_names.clear();
 
   proxy->reset();
 
@@ -1266,23 +1285,45 @@ std::istream & colvarmodule::read_restart(std::istream &is)
     // read global restart information
     std::string restart_conf;
     if (is >> colvarparse::read_block("configuration", restart_conf)) {
+
       parse->get_keyval(restart_conf, "step",
                         it_restart, static_cast<step_number>(0),
                         colvarparse::parse_restart);
       it = it_restart;
+
       std::string restart_version;
+      int restart_version_int = 0;
       parse->get_keyval(restart_conf, "version",
                         restart_version, std::string(""),
                         colvarparse::parse_restart);
-      if (restart_version.size() && (restart_version != std::string(COLVARS_VERSION))) {
+      if (restart_version.size()) {
-        cvm::log("This state file was generated with version "+restart_version+"\n");
+        if (restart_version != std::string(COLVARS_VERSION)) {
+          cvm::log("This state file was generated with version "+
+                   restart_version+"\n");
         }
-      if ((restart_version.size() == 0) || (restart_version.compare(std::string(COLVARS_VERSION)) < 0)) {
+        restart_version_int =
+          proxy->get_version_from_string(restart_version.c_str());
+      }
+
+      if (restart_version_int < 20160810) {
         // check for total force change
         if (proxy->total_forces_enabled()) {
           warn_total_forces = true;
         }
       }
+
+      std::string units_restart;
+      if (parse->get_keyval(restart_conf, "units",
+                            units_restart, std::string(""),
+                            colvarparse::parse_restart)) {
+        units_restart = colvarparse::to_lower_cppstr(units_restart);
+        if ((proxy->units.size() > 0) && (units_restart != proxy->units)) {
+          cvm::error("Error: the state file has units \""+units_restart+
+                     "\", but the current unit system is \""+proxy->units+
+                     "\".\n", INPUT_ERROR);
+        }
+      }
+
     }
     is.clear();
     parse->clear_keyword_registry();
@@ -1314,69 +1355,19 @@ std::istream & colvarmodule::read_restart(std::istream &is)
 
   if (warn_total_forces) {
     cvm::log(cvm::line_marker);
-    cvm::log("WARNING:\n");
+    cvm::log("WARNING: The definition of system forces has changed.  Please see:\n");
-    std::string const warning("### CHANGES IN THE DEFINITION OF SYSTEM FORCES (NOW TOTAL FORCES)\n\
+    cvm::log("  https://colvars.github.io/README-totalforce.html\n");
-\n\
-Starting from the version 2016-08-10 of the Colvars module, \n\
-the role of system forces has been replaced by total forces.\n\
-\n\
-These include *all* forces acting on a collective variable, whether they\n\
-come from the force field potential or from external terms\n\
-(e.g. restraints), including forces applied by Colvars itself.\n\
-\n\
-In NAMD, forces applied by Colvars, IMD, SMD, TMD, symmetry\n\
-restraints and tclForces are now all counted in the total force.\n\
-\n\
-In LAMMPS, forces applied by Colvars itself are now counted in the total\n\
-force (all forces from other fixes were being counted already).\n\
-\n\
-\n\
-### WHEN IS THIS CHANGE RELEVANT\n\
-\n\
-This change affects results *only* when (1) outputSystemForce is\n\
-requested or (2) the ABF bias is used.  All other usage cases are\n\
-*unaffected* (colvar restraints, metadynamics, etc).\n\
-\n\
-When system forces are reported (flag: outputSystemForce), their values\n\
-in the output may change, but the physical trajectory is never affected.\n\
-The physical results of ABF calculations may be affected in some cases.\n\
-\n\
-\n\
-### CHANGES TO ABF CALCULATIONS\n\
-\n\
-Compared to previous Colvars versions, the ABF method will now attempt\n\
-to cancel external forces (for example, boundary walls) and it may be\n\
-not possible to resume through a state file a simulation that was\n\
-performed with a previous version.\n\
-\n\
-There are three possible scenarios:\n\
-\n\
-1. No external forces are applied to the atoms used by ABF: results are\n\
-unchanged.\n\
-\n\
-2. Some of the atoms used by ABF experience external forces, but these\n\
-forces are not applied directly to the variables used by ABF\n\
-(e.g. another colvar that uses the same atoms, tclForces, etc): in this\n\
-case, we recommend beginning a new simulation.\n\
-\n\
-3. External forces are applied to one or more of the colvars used by\n\
-ABF, but no other forces are applied to their atoms: you may use the\n\
-subtractAppliedForce keyword inside the corresponding colvars to\n\
-continue the previous simulation.\n\n");
-    cvm::log(warning);
-    cvm::log(cvm::line_marker);
-
     // update this ahead of time in this special case
     output_prefix() = proxy->input_prefix();
     cvm::log("All output files will now be saved with the prefix \""+output_prefix()+".tmp.*\".\n");
-    cvm::log(cvm::line_marker);
     cvm::log("Please review the important warning above. After that, you may rename:\n\
 \""+output_prefix()+".tmp.colvars.state\"\n\
 to:\n\
-\""+ proxy->input_prefix()+".colvars.state\"\n");
+\""+proxy->input_prefix()+".colvars.state\"\n\
+and load it to continue this simulation.\n");
     output_prefix() = output_prefix()+".tmp";
     write_restart_file(output_prefix()+".colvars.state");
-    cvm::error("Exiting with error until issue is addressed.\n", FATAL_ERROR);
+    cvm::error("Exiting with error until issue is addressed.\n", INPUT_ERROR);
   }
 
   return is;
@@ -1496,8 +1487,11 @@ std::ostream & colvarmodule::write_restart(std::ostream &os)
      << "  step " << std::setw(it_width)
      << it << "\n"
      << "  dt " << dt() << "\n"
-     << "  version " << std::string(COLVARS_VERSION) << "\n"
+     << "  version " << std::string(COLVARS_VERSION) << "\n";
-     << "}\n\n";
+  if (proxy->units.size() > 0) {
+    os << "  units " << proxy->units << "\n";
+  }
+  os << "}\n\n";
 
   int error_code = COLVARS_OK;
 
@@ -1718,32 +1712,61 @@ int cvm::read_index_file(char const *filename)
   while (is.good()) {
     char open, close;
     std::string group_name;
+    int index_of_group = -1;
     if ( (is >> open) && (open == '[') &&
          (is >> group_name) &&
          (is >> close) && (close == ']') ) {
-      for (std::list<std::string>::iterator names_i = index_group_names.begin();
+      size_t i = 0;
-           names_i != index_group_names.end();
+      for ( ; i < index_group_names.size(); i++) {
-           names_i++) {
+        if (index_group_names[i] == group_name) {
-        if (*names_i == group_name) {
+          // Found a group with the same name
-          cvm::error("Error: the group name \""+group_name+
+          index_of_group = i;
-                     "\" appears in multiple index files.\n",
-                     FILE_ERROR);
         }
       }
+      if (index_of_group < 0) {
         index_group_names.push_back(group_name);
-      index_groups.push_back(std::vector<int>());
+        index_groups.push_back(NULL);
+        index_of_group = index_groups.size()-1;
+      }
     } else {
-      cvm::error("Error: in parsing index file \""+
+      return cvm::error("Error: in parsing index file \""+
                         std::string(filename)+"\".\n",
                         INPUT_ERROR);
     }
 
+    std::vector<int> *old_index_group = index_groups[index_of_group];
+    std::vector<int> *new_index_group = new std::vector<int>();
+
     int atom_number = 1;
     size_t pos = is.tellg();
     while ( (is >> atom_number) && (atom_number > 0) ) {
-      (index_groups.back()).push_back(atom_number);
+      new_index_group->push_back(atom_number);
       pos = is.tellg();
     }
+
+    if (old_index_group != NULL) {
+      bool equal = false;
+      if (new_index_group->size() == old_index_group->size()) {
+        if (std::equal(new_index_group->begin(), new_index_group->end(),
+                       old_index_group->begin())) {
+          equal = true;
+        }
+      }
+      if (! equal) {
+        new_index_group->clear();
+        delete new_index_group;
+        new_index_group = NULL;
+        return cvm::error("Error: the index group \""+group_name+
+                          "\" was redefined.\n", INPUT_ERROR);
+      } else {
+        old_index_group->clear();
+        delete old_index_group;
+        old_index_group = NULL;
+      }
+    }
+
+    index_groups[index_of_group] = new_index_group;
+
     is.clear();
     is.seekg(pos, std::ios::beg);
     std::string delim;
@@ -1756,14 +1779,27 @@ int cvm::read_index_file(char const *filename)
     }
   }
 
-  cvm::log("The following index groups were read from the index file \""+
+  cvm::log("The following index groups are currently defined:\n");
-           std::string(filename)+"\":\n");
+  size_t i = 0;
-  std::list<std::string>::iterator names_i = index_group_names.begin();
+  for ( ; i < index_group_names.size(); i++) {
-  std::list<std::vector<int> >::iterator lists_i = index_groups.begin();
+    cvm::log("  "+(index_group_names[i])+" ("+
-  for ( ; names_i != index_group_names.end() ; names_i++, lists_i++) {
+             cvm::to_str((index_groups[i])->size())+" atoms)\n");
-    cvm::log("  "+(*names_i)+" ("+cvm::to_str(lists_i->size())+" atoms).\n");
   }
-  return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
+
+  return COLVARS_OK;
+}
+
+
+int colvarmodule::reset_index_groups()
+{
+  size_t i = 0;
+  for ( ; i < index_groups.size(); i++) {
+    delete index_groups[i];
+    index_groups[i] = NULL;
+  }
+  index_group_names.clear();
+  index_groups.clear();
+  return COLVARS_OK;
 }
 
 
@@ -1799,7 +1835,7 @@ int cvm::load_coords(char const *file_name,
                         "for XYZ coordinate files.\n", INPUT_ERROR);
     }
     // For XYZ files, use internal parser
-    error_code |= cvm::load_coords_xyz(file_name, &sorted_pos, atoms);
+    error_code |= cvm::main()->load_coords_xyz(file_name, &sorted_pos, atoms);
   } else {
     // Otherwise, call proxy function for PDB
     error_code |= proxy->load_coords(file_name,
@@ -1824,11 +1860,18 @@ int cvm::load_coords_xyz(char const *filename,
   unsigned int natoms;
   char symbol[256];
   std::string line;
+  cvm::real x = 0.0, y = 0.0, z = 0.0;
 
   if ( ! (xyz_is >> natoms) ) {
     cvm::error("Error: cannot parse XYZ file "
                + std::string(filename) + ".\n", INPUT_ERROR);
   }
+
+  ++xyz_reader_use_count;
+  if (xyz_reader_use_count < 2) {
+    cvm::log("Warning: beginning from 2019-11-26 the XYZ file reader assumes Angstrom units.");
+  }
+
   // skip comment line
   cvm::getline(xyz_is, line);
   cvm::getline(xyz_is, line);
@@ -1845,12 +1888,19 @@ int cvm::load_coords_xyz(char const *filename,
         next++;
       }
       xyz_is >> symbol;
-      xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
+      xyz_is >> x >> y >> z;
+      // XYZ files are assumed to be in Angstrom (as eg. VMD will)
+      (*pos_i)[0] = proxy->angstrom_to_internal(x);
+      (*pos_i)[1] = proxy->angstrom_to_internal(y);
+      (*pos_i)[2] = proxy->angstrom_to_internal(z);
     }
   } else {          // Use all positions
     for ( ; pos_i != pos->end() ; pos_i++) {
       xyz_is >> symbol;
-      xyz_is >> (*pos_i)[0] >> (*pos_i)[1] >> (*pos_i)[2];
+      xyz_is >> x >> y >> z;
+      (*pos_i)[0] = proxy->angstrom_to_internal(x);
+      (*pos_i)[1] = proxy->angstrom_to_internal(y);
+      (*pos_i)[2] = proxy->angstrom_to_internal(z);
     }
   }
   return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK);
@@ -1860,11 +1910,6 @@ int cvm::load_coords_xyz(char const *filename,
 
 // Wrappers to proxy functions: these may go in the future
 
-cvm::real cvm::unit_angstrom()
-{
-  return proxy->unit_angstrom();
-}
-
 
 cvm::real cvm::boltzmann()
 {
@@ -1903,39 +1948,6 @@ cvm::real cvm::rand_gaussian(void)
 }
 
 
-
-bool cvm::replica_enabled()
-{
-  return proxy->replica_enabled();
-}
-
-int cvm::replica_index()
-{
-  return proxy->replica_index();
-}
-
-int cvm::replica_num()
-{
-  return proxy->replica_num();
-}
-
-void cvm::replica_comm_barrier()
-{
-  return proxy->replica_comm_barrier();
-}
-
-int cvm::replica_comm_recv(char* msg_data, int buf_len, int src_rep)
-{
-  return proxy->replica_comm_recv(msg_data,buf_len,src_rep);
-}
-
-int cvm::replica_comm_send(char* msg_data, int msg_len, int dest_rep)
-{
-  return proxy->replica_comm_send(msg_data,msg_len,dest_rep);
-}
-
-
-
 template<typename T> std::string _to_str(T const &x,
                                          size_t width, size_t prec)
 {

lib/colvars/colvarmodule.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -608,10 +608,6 @@ public:
 
   // proxy functions
 
-  /// \brief Value of the unit for atomic coordinates with respect to
-  /// angstroms (used by some variables for hard-coded default values)
-  static real unit_angstrom();
-
   /// \brief Boltmann constant
   static real boltzmann();
 
@@ -678,29 +674,23 @@ public:
     return 5;
   }
 
-
-  // Replica exchange commands.
-  static bool replica_enabled();
-  static int replica_index();
-  static int replica_num();
-  static void replica_comm_barrier();
-  static int replica_comm_recv(char* msg_data, int buf_len, int src_rep);
-  static int replica_comm_send(char* msg_data, int msg_len, int dest_rep);
-
   /// \brief Get the distance between two atomic positions with pbcs handled
   /// correctly
   static rvector position_distance(atom_pos const &pos1,
                                    atom_pos const &pos2);
 
-  /// \brief Names of groups from a Gromacs .ndx file to be read at startup
+  /// \brief Names of groups from one or more Gromacs .ndx files
-  std::list<std::string> index_group_names;
+  std::vector<std::string> index_group_names;
 
-  /// \brief Groups from a Gromacs .ndx file read at startup
+  /// \brief Groups from one or more Gromacs .ndx files
-  std::list<std::vector<int> > index_groups;
+  std::vector<std::vector<int> *> index_groups;
 
   /// \brief Read a Gromacs .ndx file
   int read_index_file(char const *filename);
 
+  /// Clear the index groups loaded so far
+  int reset_index_groups();
+
   /// \brief Select atom IDs from a file (usually PDB) \param filename name of
   /// the file \param atoms array into which atoms read from "filename" will be
   /// appended \param pdb_field (optional) if the file is a PDB and this
@@ -726,9 +716,8 @@ public:
                          std::string const &pdb_field,
                          double pdb_field_value = 0.0);
 
-  /// \brief Load the coordinates for a group of atoms from an
+  /// Load coordinates into an atom group from an XYZ file (assumes Angstroms)
-  /// XYZ file
+  int load_coords_xyz(char const *filename,
-  static int load_coords_xyz(char const *filename,
                       std::vector<rvector> *pos,
                       atom_group *atoms);
 
@@ -771,6 +760,9 @@ private:
   /// Thread-specific depth
   std::vector<size_t> depth_v;
 
+  /// Track how many times the XYZ reader has been used
+  int xyz_reader_use_count;
+
 public:
 
   /// Get the current object depth in the hierarchy

lib/colvars/colvarparams.cpp

@@ -0,0 +1,111 @@
+// -*- c++ -*-
+
+// 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 <sstream>
+#include <iostream>
+#include <algorithm>
+
+#include "colvarmodule.h"
+#include "colvarvalue.h"
+#include "colvarparams.h"
+
+
+
+colvarparams::colvarparams()
+{}
+
+
+colvarparams::~colvarparams()
+{}
+
+
+void colvarparams::register_param(std::string const &param_name,
+                                  void *param_ptr)
+{
+  param_map[param_name] = param_ptr;
+}
+
+
+void colvarparams::register_param_grad(std::string const &param_name,
+                                       colvarvalue *param_grad_ptr)
+{
+  param_grad_map[param_name] = param_grad_ptr;
+}
+
+
+int colvarparams::param_exists(std::string const &param_name)
+{
+  if (param_map.count(param_name) > 0) {
+    return COLVARS_OK;
+  }
+  return INPUT_ERROR;
+}
+
+
+std::vector<std::string> colvarparams::get_param_names()
+{
+  std::vector<std::string> result;
+  for (std::map<std::string, void const *>::const_iterator elem =
+         param_map.begin(); elem != param_map.end(); elem++) {
+    result.push_back(elem->first);
+  }
+  return result;
+}
+
+
+std::vector<std::string> colvarparams::get_param_grad_names()
+{
+  std::vector<std::string> result;
+  for (std::map<std::string, colvarvalue const *>::const_iterator elem =
+         param_grad_map.begin(); elem != param_grad_map.end(); elem++) {
+    result.push_back(elem->first);
+  }
+  return result;
+}
+
+
+void const *colvarparams::get_param_ptr(std::string const &param_name)
+{
+  if (param_map.count(param_name) > 0) {
+    return param_map[param_name];
+  }
+  cvm::error("Error: parameter \""+param_name+"\" not found.\n", INPUT_ERROR);
+  return NULL;
+}
+
+
+void const *colvarparams::get_param_grad_ptr(std::string const &param_name)
+{
+  if (param_grad_map.count(param_name) > 0) {
+    return param_grad_map[param_name];
+  }
+  cvm::error("Error: gradient of parameter \""+param_name+"\" not found.\n",
+             INPUT_ERROR);
+  return NULL;
+}
+
+
+cvm::real colvarparams::get_param(std::string const &param_name)
+{
+  cvm::real const *ptr =
+    reinterpret_cast<cvm::real const *>(get_param_ptr(param_name));
+  return ptr != NULL ? *ptr : 0.0;
+}
+
+
+int colvarparams::set_param(std::string const &param_name,
+                            void const *new_value)
+{
+  if (param_map.count(param_name) > 0) {
+    return cvm::error("Error: parameter \""+param_name+"\" cannot be "
+                      "modified.\n", COLVARS_NOT_IMPLEMENTED);
+  }
+  return cvm::error("Error: parameter \""+param_name+"\" not found.\n",
+                    INPUT_ERROR);
+}

lib/colvars/colvarparams.h

@@ -0,0 +1,66 @@
+// -*- c++ -*-
+
+// 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.
+
+#ifndef COLVARPARAMS_H
+#define COLVARPARAMS_H
+
+#include <map>
+
+/// \file colvarparams.h Functions to handle scalar parameters used in objects
+
+
+class colvarparams {
+
+ public:
+
+  /// Whether the parameter param_name exists
+  int param_exists(std::string const &param_name);
+
+  /// Get a copy of the names of registered parameters
+  virtual std::vector<std::string> get_param_names();
+
+  /// Get a copy of the names of registered parameter gradients
+  virtual std::vector<std::string> get_param_grad_names();
+
+  /// Pointer to the parameter param_name
+  virtual void const *get_param_ptr(std::string const &param_name);
+
+  /// Pointer to the gradient of parameter param_name
+  virtual void const *get_param_grad_ptr(std::string const &param_name);
+
+  /// Value of the parameter param_name (must be a scalar)
+  virtual cvm::real get_param(std::string const &param_name);
+
+  /// Set the named parameter to the given value
+  virtual int set_param(std::string const &param_name, void const *new_value);
+
+ protected:
+
+  /// Default constructor
+  colvarparams();
+
+  /// Default destructor
+  virtual ~colvarparams();
+
+  /// Pointers to relevant parameters that may be accessed by other objects
+  std::map<std::string, void const *> param_map;
+
+  /// Derivatives of the object with respect to internal parameters
+  std::map<std::string, colvarvalue const *> param_grad_map;
+
+  /// Register the given parameter
+  void register_param(std::string const &param_name, void *param_ptr);
+
+  /// Register the gradient of the given parameter
+  void register_param_grad(std::string const &param_name,
+                           colvarvalue *param_grad_ptr);
+
+};
+
+#endif

lib/colvars/colvarparse.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -32,6 +32,41 @@ namespace {
 }
 
 
+colvarparse::colvarparse()
+{
+  init();
+}
+
+
+void colvarparse::init()
+{
+  config_string.clear();
+  clear_keyword_registry();
+}
+
+
+colvarparse::colvarparse(const std::string& conf)
+{
+  init(conf);
+}
+
+
+void colvarparse::init(std::string const &conf)
+{
+  if (! config_string.size()) {
+    init();
+    config_string = conf;
+  }
+}
+
+
+colvarparse::~colvarparse()
+{
+  init();
+}
+
+
+
 bool colvarparse::get_key_string_value(std::string const &conf,
                                        char const *key, std::string &data)
 {
@@ -156,7 +191,7 @@ template<>
 int colvarparse::_get_keyval_scalar_value_(std::string const &key_str,
                                            std::string const &data,
                                            bool &value,
-                                           bool const &def_value)
+                                           bool const & /* def_value */)
 {
   if ( (data == std::string("on")) ||
        (data == std::string("yes")) ||
@@ -176,8 +211,8 @@ int colvarparse::_get_keyval_scalar_value_(std::string const &key_str,
 
 template<typename TYPE>
 int colvarparse::_get_keyval_scalar_novalue_(std::string const &key_str,
-                                             TYPE &value,
+                                             TYPE & /* value */,
-                                             Parse_Mode const &parse_mode)
+                                             Parse_Mode const & /* parse_mode */)
 {
   return cvm::error("Error: improper or missing value "
                     "for \""+key_str+"\".\n", INPUT_ERROR);

lib/colvars/colvarparse.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -12,10 +12,10 @@
 
 #include <cstring>
 #include <string>
-#include <map>
 
 #include "colvarmodule.h"
 #include "colvarvalue.h"
+#include "colvarparams.h"
 
 
 /// \file colvarparse.h Parsing functions for collective variables
@@ -23,37 +23,24 @@
 
 /// \brief Base class containing parsing functions; all objects which
 /// need to parse input inherit from this
-class colvarparse {
+class colvarparse : public colvarparams {
 
 public:
 
   /// Default constructor
-  inline colvarparse()
+  colvarparse();
-  {
-    init();
-  }
 
   /// Constructor that stores the object's config string
-  inline colvarparse(const std::string& conf)
+  colvarparse(const std::string& conf);
-  {
-    init(conf);
-  }
 
   /// Set the object ready to parse a new configuration string
-  inline void init()
+  void init();
-  {
-    config_string.clear();
-    clear_keyword_registry();
-  }
 
   /// Set a new config string for this object
-  inline void init(std::string const &conf)
+  void init(std::string const &conf);
-  {
+
-    if (! config_string.size()) {
+  /// Default destructor
-      init();
+  virtual ~colvarparse();
-      config_string = conf;
-    }
-  }
 
   /// Get the configuration string (includes comments)
   inline std::string const & get_config() const

lib/colvars/colvarproxy.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -33,6 +33,7 @@
 
 
 colvarproxy_system::colvarproxy_system()
+  : angstrom_value(0.)
 {
   reset_pbc_lattice();
 }
@@ -41,7 +42,7 @@ colvarproxy_system::colvarproxy_system()
 colvarproxy_system::~colvarproxy_system() {}
 
 
-void colvarproxy_system::add_energy(cvm::real energy) {}
+void colvarproxy_system::add_energy(cvm::real /* energy */) {}
 
 
 void colvarproxy_system::request_total_force(bool yesno)
@@ -173,9 +174,9 @@ int colvarproxy_atoms::add_atom_slot(int atom_id)
 }
 
 
-int colvarproxy_atoms::init_atom(cvm::residue_id const &residue,
+int colvarproxy_atoms::init_atom(cvm::residue_id const & /* residue */,
-                                 std::string const     &atom_name,
+                                 std::string const     & /* atom_name */,
-                                 std::string const     &segment_id)
+                                 std::string const     & /* segment_id */)
 {
   cvm::error("Error: initializing an atom by name and residue number is currently not supported.\n",
              COLVARS_NOT_IMPLEMENTED);
@@ -204,9 +205,9 @@ void colvarproxy_atoms::clear_atom(int index)
 }
 
 
-int colvarproxy_atoms::load_atoms(char const *filename,
+int colvarproxy_atoms::load_atoms(char const * /* filename */,
-                                  cvm::atom_group &atoms,
+                                  cvm::atom_group & /* atoms */,
-                                  std::string const &pdb_field,
+                                  std::string const & /* pdb_field */,
                                   double)
 {
   return cvm::error("Error: loading atom identifiers from a file "
@@ -215,10 +216,10 @@ int colvarproxy_atoms::load_atoms(char const *filename,
 }
 
 
-int colvarproxy_atoms::load_coords(char const *filename,
+int colvarproxy_atoms::load_coords(char const * /* filename */,
-                                   std::vector<cvm::atom_pos> &pos,
+                                   std::vector<cvm::atom_pos> & /* pos */,
-                                   std::vector<int> const &sorted_ids,
+                                   std::vector<int> const & /* sorted_ids */,
-                                   std::string const &pdb_field,
+                                   std::string const & /* pdb_field */,
                                    double)
 {
   return cvm::error("Error: loading atomic coordinates from a file "
@@ -269,7 +270,7 @@ int colvarproxy_atom_groups::scalable_group_coms()
 }
 
 
-int colvarproxy_atom_groups::init_atom_group(std::vector<int> const &atoms_ids)
+int colvarproxy_atom_groups::init_atom_group(std::vector<int> const & /* atoms_ids */)
 {
   cvm::error("Error: initializing a group outside of the Colvars module "
              "is currently not supported.\n",
@@ -456,51 +457,6 @@ int colvarproxy_smp::smp_unlock()
 
 
 
-colvarproxy_replicas::colvarproxy_replicas() {}
-
-
-colvarproxy_replicas::~colvarproxy_replicas() {}
-
-
-bool colvarproxy_replicas::replica_enabled()
-{
-  return false;
-}
-
-
-int colvarproxy_replicas::replica_index()
-{
-  return 0;
-}
-
-
-int colvarproxy_replicas::replica_num()
-{
-  return 1;
-}
-
-
-void colvarproxy_replicas::replica_comm_barrier() {}
-
-
-int colvarproxy_replicas::replica_comm_recv(char* msg_data,
-                                            int buf_len,
-                                            int src_rep)
-{
-  return COLVARS_NOT_IMPLEMENTED;
-}
-
-
-int colvarproxy_replicas::replica_comm_send(char* msg_data,
-                                            int msg_len,
-                                            int dest_rep)
-{
-  return COLVARS_NOT_IMPLEMENTED;
-}
-
-
-
-
 colvarproxy_script::colvarproxy_script()
 {
   script = NULL;
@@ -518,7 +474,7 @@ char const *colvarproxy_script::script_obj_to_str(unsigned char *obj)
 }
 
 
-std::vector<std::string> colvarproxy_script::script_obj_to_str_vector(unsigned char *obj)
+std::vector<std::string> colvarproxy_script::script_obj_to_str_vector(unsigned char * /* obj */)
 {
   cvm::error("Error: trying to print a script object without a scripting "
              "language interface.\n", BUG_ERROR);
@@ -532,19 +488,17 @@ int colvarproxy_script::run_force_callback()
 }
 
 
-int colvarproxy_script::run_colvar_callback(
+int colvarproxy_script::run_colvar_callback(std::string const & /* name */,
-      std::string const &name,
+					    std::vector<const colvarvalue *> const & /* cvcs */,
-      std::vector<const colvarvalue *> const &cvcs,
+					    colvarvalue & /* value */)
-      colvarvalue &value)
 {
   return COLVARS_NOT_IMPLEMENTED;
 }
 
 
-int colvarproxy_script::run_colvar_gradient_callback(
+int colvarproxy_script::run_colvar_gradient_callback(std::string const & /* name */,
-      std::string const &name,
+						     std::vector<const colvarvalue *> const & /* cvcs */,
-      std::vector<const colvarvalue *> const &cvcs,
+						     std::vector<cvm::matrix2d<cvm::real> > & /* gradient */)
-      std::vector<cvm::matrix2d<cvm::real> > &gradient)
 {
   return COLVARS_NOT_IMPLEMENTED;
 }
@@ -599,9 +553,9 @@ int colvarproxy_tcl::tcl_run_force_callback()
 
 
 int colvarproxy_tcl::tcl_run_colvar_callback(
-                         std::string const &name,
+					     std::string const & name,
-                         std::vector<const colvarvalue *> const &cvc_values,
+					     std::vector<const colvarvalue *> const & cvc_values,
-                         colvarvalue &value)
+					     colvarvalue & value)
 {
 #if defined(COLVARS_TCL)
 
@@ -636,9 +590,9 @@ int colvarproxy_tcl::tcl_run_colvar_callback(
 
 
 int colvarproxy_tcl::tcl_run_colvar_gradient_callback(
-                         std::string const &name,
+						      std::string const & name,
-                         std::vector<const colvarvalue *> const &cvc_values,
+						      std::vector<const colvarvalue *> const & cvc_values,
-                         std::vector<cvm::matrix2d<cvm::real> > &gradient)
+						      std::vector<cvm::matrix2d<cvm::real> > & gradient)
 {
 #if defined(COLVARS_TCL)
 
@@ -776,7 +730,7 @@ int colvarproxy_io::close_output_stream(std::string const &output_name)
 }
 
 
-int colvarproxy_io::backup_file(char const *filename)
+int colvarproxy_io::backup_file(char const * /* filename */)
 {
   // TODO implement this using rename_file()
   return COLVARS_NOT_IMPLEMENTED;
@@ -785,12 +739,32 @@ int colvarproxy_io::backup_file(char const *filename)
 
 int colvarproxy_io::remove_file(char const *filename)
 {
+  int error_code = COLVARS_OK;
+#if defined(WIN32) && !defined(__CYGWIN__)
+  // Because the file may be open by other processes, rename it to filename.old
+  std::string const renamed_file(std::string(filename)+".old");
+  // It may still be there from an interrupted run, so remove it to be safe
+  std::remove(renamed_file.c_str());
+  int rename_exit_code = 0;
+  while ((rename_exit_code = std::rename(filename,
+                                         renamed_file.c_str())) != 0) {
+    if (errno == EINTR) continue;
+    error_code |= FILE_ERROR;
+    break;
+  }
+  // Ask to remove filename.old, but ignore any errors raised
+  std::remove(renamed_file.c_str());
+#else
   if (std::remove(filename)) {
     if (errno != ENOENT) {
+      error_code |= FILE_ERROR;
+    }
+  }
+#endif
+  if (error_code != COLVARS_OK) {
     return cvm::error("Error: in removing file \""+std::string(filename)+
                       "\".\n.",
-                        FILE_ERROR);
+                      error_code);
-    }
   }
   return COLVARS_OK;
 }

lib/colvars/colvarproxy.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -48,11 +48,45 @@ public:
   /// Destructor
   virtual ~colvarproxy_system();
 
-  /// \brief Value of the unit for atomic coordinates with respect to
+  /// \brief Name of the unit system used internally by Colvars (by default, that of the back-end).
-  /// angstroms (used by some variables for hard-coded default values)
+  /// Supported depending on the back-end: real (A, kcal/mol), metal (A, eV), electron (Bohr, Hartree), gromacs (nm, kJ/mol)
-  virtual cvm::real unit_angstrom() = 0;
+  /// Note: calls to back-end PBC functions assume back-end length unit
+  /// We use different unit from back-end in VMD bc using PBC functions from colvarproxy base class
+  /// Colvars internal units are user specified, because the module exchanges info in unknown
+  /// composite dimensions with user input, while it only exchanges quantities of known
+  /// dimension with the back-end (length and forces)
+  std::string units;
 
-  /// \brief Boltzmann constant
+  /// \brief Request to set the units used internally by Colvars
+  virtual int set_unit_system(std::string const &units, bool check_only) = 0;
+
+  /// \brief Value of 1 Angstrom in the internal (front-end) Colvars unit for atomic coordinates
+  /// * defaults to 0. in the base class; derived proxy classes must set it
+  /// * in VMD proxy, can only be changed when no variables are defined
+  /// as user-defined values in composite units must be compatible with that system
+  cvm::real angstrom_value;
+
+  /// \brief Value of 1 Angstrom in the backend's unit for atomic coordinates
+  virtual cvm::real backend_angstrom_value() = 0;
+
+  /// \brief Value of 1 kcal/mol in the internal Colvars unit for energy
+  cvm::real kcal_mol_value;
+
+  /// \brief Convert a length from Angstrom to internal
+  inline cvm::real angstrom_to_internal(cvm::real l) const
+  {
+    return l * angstrom_value;
+  }
+
+  // /// \brief Convert a length from back-end unit to internal
+  // inline cvm::real back_end_to_internal_unit(cvm::real l) {
+  //   if (angstrom_value == 0.) {
+  //     return l / backend_angstrom_value();
+  //   }
+  //   return l * angstrom_value / backend_angstrom_value();
+  // }
+
+  /// \brief Boltzmann constant in internal Colvars units
   virtual cvm::real boltzmann() = 0;
 
   /// \brief Target temperature of the simulation (K units)
@@ -212,7 +246,7 @@ public:
   }
 
   /// Read the current velocity of the given atom
-  inline cvm::rvector get_atom_velocity(int index)
+  inline cvm::rvector get_atom_velocity(int /* index */)
   {
     cvm::error("Error: reading the current velocity of an atom "
                "is not yet implemented.\n",
@@ -355,7 +389,7 @@ public:
   }
 
   /// Read the current velocity of the given atom group
-  inline cvm::rvector get_atom_group_velocity(int index)
+  inline cvm::rvector get_atom_group_velocity(int /* index */)
   {
     cvm::error("Error: reading the current velocity of an atom group is not yet implemented.\n",
                COLVARS_NOT_IMPLEMENTED);
@@ -446,15 +480,15 @@ public:
   virtual ~colvarproxy_replicas();
 
   /// \brief Indicate if multi-replica support is available and active
-  virtual bool replica_enabled();
+  virtual int replica_enabled();
 
   /// \brief Index of this replica
   virtual int replica_index();
 
-  /// \brief Total number of replica
+  /// \brief Total number of replicas
-  virtual int replica_num();
+  virtual int num_replicas();
 
-  /// \brief Synchronize replica
+  /// \brief Synchronize replica with others
   virtual void replica_comm_barrier();
 
   /// \brief Receive data from other replica
@@ -591,10 +625,10 @@ public:
     return backup_file(filename.c_str());
   }
 
-  /// Remove the given file
+  /// Remove the given file (on Windows only, rename to filename.old)
   int remove_file(char const *filename);
 
-  /// Remove the given file
+  /// Remove the given file (on Windows only, rename to filename.old)
   inline int remove_file(std::string const &filename)
   {
     return remove_file(filename.c_str());

lib/colvars/colvarproxy_replicas.cpp

@@ -0,0 +1,56 @@
+// -*- c++ -*-
+
+// 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 "colvarmodule.h"
+#include "colvarproxy.h"
+
+
+colvarproxy_replicas::colvarproxy_replicas() {}
+
+
+colvarproxy_replicas::~colvarproxy_replicas() {}
+
+
+int colvarproxy_replicas::replica_enabled()
+{
+  return COLVARS_NOT_IMPLEMENTED;
+}
+
+
+int colvarproxy_replicas::replica_index()
+{
+  return 0;
+}
+
+
+int colvarproxy_replicas::num_replicas()
+{
+  return 1;
+}
+
+
+void colvarproxy_replicas::replica_comm_barrier() {}
+
+
+int colvarproxy_replicas::replica_comm_recv(char* /* msg_data */,
+                                            int /* buf_len */,
+                                            int /* src_rep */)
+{
+  return COLVARS_NOT_IMPLEMENTED;
+}
+
+
+int colvarproxy_replicas::replica_comm_send(char* /* msg_data */,
+                                            int /* msg_len */,
+                                            int /* dest_rep */)
+{
+  return COLVARS_NOT_IMPLEMENTED;
+}
+
+

lib/colvars/colvars_version.h

@@ -1,10 +1,3 @@
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2019-08-05"
+#define COLVARS_VERSION "2020-01-27"
-// 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.
-
 #endif

lib/colvars/colvarscript.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvarscript.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -86,6 +86,7 @@ public:
     cv_printframe,
     cv_printframelabels,
     cv_frame,
+    cv_units,
     cv_colvar,
     cv_colvar_value,
     cv_colvar_update,
@@ -269,9 +270,7 @@ extern "C" {
            "Clear the index groups loaded so far, allowing to replace them",
            0, 0,
            { },
-           cvm::main()->index_group_names.clear();
+           return cvm::main()->reset_index_groups();
-           cvm::main()->index_groups.clear();
-           return COLVARS_OK;
            )
 
   CVSCRIPT(cv_addenergy,
@@ -292,6 +291,18 @@ extern "C" {
            return COLVARS_OK;
            )
 
+  CVSCRIPT(cv_units,
+           "Get the current Colvars unit system",
+           0, 1,
+           { },
+           if (objc < 3) {
+            script->set_str_result(cvm::proxy->units);
+            return COLVARS_OK;
+           } else {
+            return cvm::proxy->set_unit_system(script->obj_to_str(objv[2]) , false);
+           }
+           )
+
 #ifndef COLVARSCRIPT_INIT_FN
 #ifdef __cplusplus
 } // extern "C"

lib/colvars/colvartypes.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvartypes.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvarvalue.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

lib/colvars/colvarvalue.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

src/USER-COLVARS/colvarproxy_lammps.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -110,7 +110,7 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
     restart_output_prefix_str.erase(restart_output_prefix_str.rfind(".*"),2);
 
   // initialize multi-replica support, if available
-  if (replica_enabled()) {
+  if (replica_enabled() == COLVARS_OK) {
     MPI_Comm_rank(inter_comm, &inter_me);
     MPI_Comm_size(inter_comm, &inter_num);
   }
@@ -131,6 +131,11 @@ void colvarproxy_lammps::init(const char *conf_file)
            cvm::to_str(COLVARPROXY_VERSION)+".\n");
 
   my_angstrom  = _lmp->force->angstrom;
+  // Front-end unit is the same as back-end
+  angstrom_value = my_angstrom;
+
+  // my_kcal_mol  = _lmp->force->qe2f / 23.060549;
+  // force->qe2f is 1eV expressed in LAMMPS' energy unit (1 if unit is eV, 23 if kcal/mol)
   my_boltzmann = _lmp->force->boltz;
   my_timestep  = _lmp->update->dt * _lmp->force->femtosecond;
 
@@ -325,6 +330,17 @@ void colvarproxy_lammps::fatal_error(std::string const &message)
 }
 
 
+int colvarproxy_lammps::set_unit_system(std::string const &units_in, bool /*check_only*/)
+{
+  std::string lmp_units = _lmp->update->unit_style;
+  if (units_in != lmp_units) {
+    cvm::error("Error: Specified unit system for Colvars \"" + units_in + "\" is incompatible with LAMMPS internal units (" + lmp_units + ").\n");
+    return COLVARS_ERROR;
+  }
+  return COLVARS_OK;
+}
+
+
 int colvarproxy_lammps::backup_file(char const *filename)
 {
   if (std::string(filename).rfind(std::string(".colvars.state"))
@@ -338,6 +354,24 @@ int colvarproxy_lammps::backup_file(char const *filename)
 
 // multi-replica support
 
+int colvarproxy_lammps::replica_enabled()
+{
+  return (inter_comm != MPI_COMM_NULL) ? COLVARS_OK : COLVARS_NOT_IMPLEMENTED;
+}
+
+
+int colvarproxy_lammps::replica_index()
+{
+  return inter_me;
+}
+
+
+int colvarproxy_lammps::num_replicas()
+{
+  return inter_num;
+}
+
+
 void colvarproxy_lammps::replica_comm_barrier()
 {
   MPI_Barrier(inter_comm);

src/USER-COLVARS/colvarproxy_lammps.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.
@@ -48,13 +48,6 @@ class colvarproxy_lammps : public colvarproxy {
   bool total_force_requested;
   bool do_exit;
 
-  // std::vector<int>          colvars_atoms;
-  // std::vector<size_t>       colvars_atoms_ncopies;
-  // std::vector<struct commdata> positions;
-  // std::vector<struct commdata> total_forces;
-  // std::vector<struct commdata> applied_forces;
-  // std::vector<struct commdata> previous_applied_forces;
-
   std::vector<int>          atoms_types;
 
   MPI_Comm inter_comm;     // MPI comm with 1 root proc from each world
@@ -98,10 +91,11 @@ class colvarproxy_lammps : public colvarproxy {
   // read additional config from string
   void add_config_string(const std::string &config);
 
-  // implementation of pure methods from base class
+  // Request to set the units used internally by Colvars
- public:
+  int set_unit_system(std::string const &units_in, bool check_only);
+
+  inline cvm::real backend_angstrom_value() { return my_angstrom; };
 
-  inline cvm::real unit_angstrom() { return my_angstrom; };
   inline cvm::real boltzmann() { return my_boltzmann; };
   inline cvm::real temperature() { return t_target; };
   inline cvm::real dt() { return my_timestep; }; // return _lmp->update->dt * _lmp->force->femtosecond; };
@@ -127,26 +121,12 @@ class colvarproxy_lammps : public colvarproxy {
 
   inline std::vector<int> *modify_atom_types() { return &atoms_types; }
 
-  // implementation of optional methods from base class
+  virtual int replica_enabled();
- public:
+  virtual int replica_index();
+  virtual int num_replicas();
 
-  // Multi-replica support
-  // Indicate if multi-replica support is available and active
-  virtual bool replica_enabled() { return (inter_comm != MPI_COMM_NULL); }
-
-  // Index of this replica
-  virtual int replica_index() { return inter_me; }
-
-  // Total number of replica
-  virtual int replica_num() { return inter_num; }
-
-  // Synchronize replica
   virtual void replica_comm_barrier();
-
-  // Receive data from other replica
   virtual int replica_comm_recv(char* msg_data, int buf_len, int src_rep);
-
-  // Send data to other replica
   virtual int replica_comm_send(char* msg_data, int msg_len, int dest_rep);
 };
 

src/USER-COLVARS/colvarproxy_lammps_version.h

@@ -1,10 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2019-08-01"
+#define COLVARPROXY_VERSION "2019-12-04"
-// 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.
-
 #endif

src/USER-COLVARS/fix_colvars.cpp

@@ -2,7 +2,7 @@
 
 // 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
+// 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.

src/USER-COLVARS/fix_colvars.h

@@ -2,7 +2,7 @@
 
 // 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
+// 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.