update colvars to another set of changes from the upstream repo

(cherry picked from commit cb816f8cba)

lib/colvars/colvar.cpp

@@ -1952,4 +1952,4 @@ void colvar::calc_runave()
 
 // Static members
 
-std::vector<cvm::deps::feature *> colvar::cv_features;
+std::vector<colvardeps::feature *> colvar::cv_features;

lib/colvars/colvar.h

@@ -38,7 +38,7 @@
 /// \link colvarvalue \endlink type, you should also add its
 /// initialization line in the \link colvar \endlink constructor.
 
-class colvar : public colvarparse, public cvm::deps {
+class colvar : public colvarparse, public colvardeps {
 
 public:
 

lib/colvars/colvaratoms.cpp

@@ -1192,6 +1192,6 @@ void cvm::atom_group::apply_force(cvm::rvector const &force)
 
 // Static members
 
-std::vector<cvm::deps::feature *> cvm::atom_group::ag_features;
+std::vector<colvardeps::feature *> cvm::atom_group::ag_features;
 
 

lib/colvars/colvaratoms.h

@@ -139,7 +139,7 @@ public:
 /// \brief Group of \link atom \endlink objects, mostly used by a
 /// \link cvc \endlink object to gather all atomic data
 class colvarmodule::atom_group
-  : public colvarparse, public cvm::deps
+  : public colvarparse, public colvardeps
 {
 public:
 

lib/colvars/colvarbias.cpp

@@ -246,4 +246,4 @@ std::ostream & colvarbias::write_traj(std::ostream &os)
 
 // Static members
 
-std::vector<cvm::deps::feature *> colvarbias::cvb_features;
+std::vector<colvardeps::feature *> colvarbias::cvb_features;

lib/colvars/colvarbias.h

@@ -9,7 +9,7 @@
 
 
 /// \brief Collective variable bias, base class
-class colvarbias : public colvarparse, public cvm::deps {
+class colvarbias : public colvarparse, public colvardeps {
 public:
 
   /// Name of this bias

lib/colvars/colvarcomp.cpp

@@ -103,7 +103,7 @@ int colvar::cvc::setup()
   description = "cvc " + name;
 
   for (i = 0; i < atom_groups.size(); i++) {
-    add_child((cvm::deps *) atom_groups[i]);
+    add_child((colvardeps *) atom_groups[i]);
   }
 
   return COLVARS_OK;
@@ -272,4 +272,4 @@ void colvar::cvc::debug_gradients(cvm::atom_group *group)
 
 // Static members
 
-std::vector<cvm::deps::feature *> colvar::cvc::cvc_features;
+std::vector<colvardeps::feature *> colvar::cvc::cvc_features;

lib/colvars/colvarcomp.h

@@ -61,7 +61,7 @@
 /// call to e.g. apply_force().
 
 class colvar::cvc
-  : public colvarparse, public cvm::deps
+  : public colvarparse, public colvardeps
 {
 public:
 

lib/colvars/colvardeps.cpp

@@ -2,7 +2,7 @@
 #include "colvardeps.h"
 
 
-cvm::deps::~deps() {
+colvardeps::~colvardeps() {
   size_t i;
 
   for (i=0; i<feature_states.size(); i++) {
@@ -25,12 +25,12 @@ cvm::deps::~deps() {
 }
 
 
-void cvm::deps::provide(int feature_id) {
+void colvardeps::provide(int feature_id) {
   feature_states[feature_id]->available = true;
 }
 
 
-int cvm::deps::enable(int feature_id,
+int colvardeps::enable(int feature_id,
                       bool dry_run /* default: false */,
                       // dry_run: fail silently, do not enable if available
                       // flag is passed recursively to deps of this feature
@@ -193,7 +193,7 @@ int cvm::deps::enable(int feature_id,
   features()[f]->requires_alt.back()[1] = h;                                           \
   features()[f]->requires_alt.back()[2] = i
 
-void cvm::deps::init_cvb_requires() {
+void colvardeps::init_cvb_requires() {
   int i;
   if (features().size() == 0) {
     for (i = 0; i < f_cvb_ntot; i++) {
@@ -225,7 +225,7 @@ void cvm::deps::init_cvb_requires() {
 }
 
 
-void cvm::deps::init_cv_requires() {
+void colvardeps::init_cv_requires() {
   size_t i;
   if (features().size() == 0) {
     for (i = 0; i < f_cv_ntot; i++) {
@@ -342,11 +342,11 @@ void cvm::deps::init_cv_requires() {
 }
 
 
-void cvm::deps::init_cvc_requires() {
+void colvardeps::init_cvc_requires() {
   size_t i;
   // Initialize static array once and for all
   if (features().size() == 0) {
-    for (i = 0; i < cvm::deps::f_cvc_ntot; i++) {
+    for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
       features().push_back(new feature);
     }
 
@@ -384,7 +384,7 @@ void cvm::deps::init_cvc_requires() {
   // Initialize feature_states for each instance
   // default as unavailable, not enabled
   feature_states.reserve(f_cvc_ntot);
-  for (i = 0; i < cvm::deps::f_cvc_ntot; i++) {
+  for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
     feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
   }
 
@@ -392,12 +392,12 @@ void cvm::deps::init_cvc_requires() {
   // Each cvc specifies what other features are available
   feature_states[f_cvc_active]->available = true;
   feature_states[f_cvc_gradient]->available = true;
-  feature_states[f_cvc_scalable_com]->available = (proxy->scalable_group_coms() == COLVARS_OK);
+  feature_states[f_cvc_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
   feature_states[f_cvc_scalable]->available = feature_states[f_cvc_scalable_com]->available;
 }
 
 
-void cvm::deps::init_ag_requires() {
+void colvardeps::init_ag_requires() {
   size_t i;
   // Initialize static array once and for all
   if (features().size() == 0) {
@@ -428,18 +428,18 @@ void cvm::deps::init_ag_requires() {
   // Initialize feature_states for each instance
   // default as unavailable, not enabled
   feature_states.reserve(f_ag_ntot);
-  for (i = 0; i < cvm::deps::f_ag_ntot; i++) {
+  for (i = 0; i < colvardeps::f_ag_ntot; i++) {
     feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
   }
 
   // Features that are implemented (or not) by all atom groups
   feature_states[f_ag_active]->available = true;
-  feature_states[f_ag_scalable_com]->available = (proxy->scalable_group_coms() == COLVARS_OK);
+  feature_states[f_ag_scalable_com]->available = (cvm::proxy->scalable_group_coms() == COLVARS_OK);
   feature_states[f_ag_scalable]->available = feature_states[f_ag_scalable_com]->available;
 }
 
 
-void cvm::deps::print_state() {
+void colvardeps::print_state() {
   size_t i;
   cvm::log("Enabled features of " + description);
   for (i = 0; i < feature_states.size(); i++) {
@@ -456,13 +456,13 @@ void cvm::deps::print_state() {
 
 
 
-void cvm::deps::add_child(deps *child) {
+void colvardeps::add_child(colvardeps *child) {
   children.push_back(child);
-  child->parents.push_back((deps *)this);
+  child->parents.push_back((colvardeps *)this);
 }
 
 
-void cvm::deps::remove_child(deps *child) {
+void colvardeps::remove_child(colvardeps *child) {
   int i;
   bool found = false;
 
@@ -490,7 +490,7 @@ void cvm::deps::remove_child(deps *child) {
 }
 
 
-void cvm::deps::remove_all_children() {
+void colvardeps::remove_all_children() {
   size_t i;
   int j;
   bool found;

lib/colvars/colvardeps.h

@@ -16,11 +16,11 @@
 
 // It seems important to have available default to false (for safety) and enabled to false (for efficiency)
 
-class cvm::deps {
+class colvardeps {
 public:
 
-  deps() {}
-  virtual ~deps();
+  colvardeps() {}
+  virtual ~colvardeps();
 
   // Subclasses should initialize the following members:
 
@@ -29,13 +29,13 @@ public:
   /// This contains the current state of each feature for each object
   class feature_state {
   private:
-    cvm::deps *const deps_object;
+    colvardeps *const deps_object;
     int const id;
     operator int() { return 0; } // never cast as int
   public:
-    inline cvm::deps *object() const { return deps_object; }
+    inline colvardeps *object() const { return deps_object; }
     inline int feature_id() const { return id; }
-    feature_state(cvm::deps *o, int i, bool a, bool e)
+    feature_state(colvardeps *o, int i, bool a, bool e)
       : deps_object(o), id(i), available(a), enabled(e) {}
 
     /// Available means: supported, subject to dependencies as listed,
@@ -97,9 +97,9 @@ public:
   // implement this as virtual to allow overriding
   virtual std::vector<feature *>&features() = 0;
 
-  void add_child(deps *child);
+  void add_child(colvardeps *child);
 
-  void remove_child(deps *child);
+  void remove_child(colvardeps *child);
 
   /// Used before deleting an object, if not handled by that object's destructor
   /// (useful for cvcs because their children are member objects)
@@ -111,11 +111,11 @@ private:
   // pointers to objects this object depends on
   // list should be maintained by any code that modifies the object
   // this could be secured by making lists of colvars / cvcs / atom groups private and modified through accessor functions
-  std::vector<deps *> children;
+  std::vector<colvardeps *> children;
 
   // pointers to objects that depend on this object
   // the size of this array is in effect a reference counter
-  std::vector<deps *> parents;
+  std::vector<colvardeps *> parents;
 
 public:
   // disabling a feature f:
@@ -128,7 +128,7 @@ public:
 //
 //   }
 
-  // std::vector<deps *> parents; // Needed to trigger a refresh if capabilities of this object change
+  // std::vector<colvardeps *> parents; // Needed to trigger a refresh if capabilities of this object change
 
   // End of members to be initialized by subclasses
 

lib/colvars/colvarmodule.cpp

@@ -302,7 +302,7 @@ int colvarmodule::parse_biases(std::string const &conf)
   size_t i;
 
   for (i = 0; i < biases.size(); i++) {
-    biases[i]->enable(cvm::deps::f_cvb_active);
+    biases[i]->enable(colvardeps::f_cvb_active);
     if (cvm::debug())
       biases[i]->print_state();
   }
@@ -310,8 +310,8 @@ int colvarmodule::parse_biases(std::string const &conf)
   size_t n_hist_dep_biases = 0;
   std::vector<std::string> hist_dep_biases_names;
   for (i = 0; i < biases.size(); i++) {
-    if (biases[i]->is_enabled(cvm::deps::f_cvb_apply_force) &&
-        biases[i]->is_enabled(cvm::deps::f_cvb_history_dependent)) {
+    if (biases[i]->is_enabled(colvardeps::f_cvb_apply_force) &&
+        biases[i]->is_enabled(colvardeps::f_cvb_history_dependent)) {
       n_hist_dep_biases++;
       hist_dep_biases_names.push_back(biases[i]->name);
     }
@@ -531,7 +531,7 @@ int colvarmodule::calc_colvars()
 
   // Determine which colvars are active at this time step
   for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
-    (*cvi)->feature_states[cvm::deps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
+    (*cvi)->feature_states[colvardeps::f_cv_active]->enabled = (step_absolute() % (*cvi)->get_time_step_factor() == 0);
   }
 
   // if SMP support is available, split up the work
@@ -689,7 +689,7 @@ int colvarmodule::update_colvar_forces()
     cvm::log("Communicating forces from the colvars to the atoms.\n");
   cvm::increase_depth();
   for (cvi = colvars.begin(); cvi != colvars.end(); cvi++) {
-    if ((*cvi)->is_enabled(cvm::deps::f_cv_gradient)) {
+    if ((*cvi)->is_enabled(colvardeps::f_cv_gradient)) {
       if (!(*cvi)->is_enabled()) continue;
       (*cvi)->communicate_forces();
       if (cvm::get_error()) {

lib/colvars/colvarmodule.h

@@ -74,9 +74,6 @@ private:
 
 public:
 
-  /// Base class to handle mutual dependencies of most objects
-  class deps;
-
   friend class colvarproxy;
   // TODO colvarscript should be unaware of colvarmodule's internals
   friend class colvarscript;

lib/colvars/colvarparse.cpp

@@ -356,7 +356,7 @@ bool colvarparse::get_keyval(std::string const &conf,
 
 bool colvarparse::get_keyval(std::string const &conf,
                              char const *key,
-                             cvm::deps::feature_state *value,
+                             colvardeps::feature_state *value,
                              bool const &def_value,
                              Parse_Mode const parse_mode)
 {
@@ -695,7 +695,6 @@ bool colvarparse::key_lookup(std::string const &conf,
                        line+"\".\n", INPUT_ERROR);
             return false;
           }
-          size_t const old_end = line.size();
 
           line_begin = line_end;
           nl = conf.find('\n', line_begin+1);
@@ -715,8 +714,6 @@ bool colvarparse::key_lookup(std::string const &conf,
         }
       }
 
-      cvm::log("Value so far = "+line.substr(data_begin, (data_end-data_begin))+".\n");
-
       // strip the leading and trailing braces
       data_begin = line.find_first_of('{') + 1;
       data_begin = line.find_first_not_of(white_space,

lib/colvars/colvarparse.h

@@ -183,7 +183,7 @@ public:
                   Parse_Mode const parse_mode = parse_normal);
   bool get_keyval(std::string const &conf,
                   char const *key,
-                  cvm::deps::feature_state *value,
+                  colvardeps::feature_state *value,
                   bool const &def_value = false,
                   Parse_Mode const parse_mode = parse_normal);