update colvars to 2015-01-22 status

lib/colvars/colvaratoms.cpp

@@ -315,14 +315,15 @@ int cvm::atom_group::parse(std::string const &conf,
 #endif
 
   if (!b_dummy) {
+
+    // calculate total mass (TODO: this is the step that most needs deferred re-initialization)
     this->total_mass = 0.0;
     for (cvm::atom_iter ai = this->begin();
          ai != this->end(); ai++) {
       this->total_mass += ai->mass;
     }
-  }
 
-  if (!b_dummy) {
+    // whether these atoms will ever receive forces or not
     bool enable_forces = true;
     // disableForces is deprecated
     if (get_keyval(group_conf, "enableForces", enable_forces, true, mode)) {
@@ -330,6 +331,8 @@ int cvm::atom_group::parse(std::string const &conf,
     } else {
       get_keyval(group_conf, "disableForces", noforce, false, colvarparse::parse_silent);
     }
+
+    get_keyval(group_conf, "weights", weights, weights, colvarparse::parse_silent);
   }
 
   // FITTING OPTIONS

lib/colvars/colvaratoms.h

@@ -139,6 +139,9 @@ public:
   /// Allocates and populates the sorted list of atom ids
   int create_sorted_ids(void);
 
+  /// List of user-defined weights to be used by certain CVCs
+  std::vector<cvm::real> weights;
+
 
   /// \brief When updating atomic coordinates, translate them to align with the
   /// center of mass of the reference coordinates

lib/colvars/colvarbias_abf.cpp

@@ -118,7 +118,7 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
   force = new cvm::real [colvars.size()];
 
   // Construct empty grids based on the colvars
-  samples   = new colvar_grid_count    (colvars);
+  samples   = new colvar_grid_count(colvars);
   gradients = new colvar_grid_gradient(colvars);
   gradients->samples = samples;
   samples->has_parent_data = true;
@@ -126,7 +126,7 @@ colvarbias_abf::colvarbias_abf(std::string const &conf, char const *key)
   // For shared ABF, we store a second set of grids.
   // This used to be only if "shared" was defined,
   // but now we allow calling share externally (e.g. from Tcl).
-  last_samples   = new colvar_grid_count    (colvars);
+  last_samples   = new colvar_grid_count(colvars);
   last_gradients = new colvar_grid_gradient(colvars);
   last_gradients->samples = last_samples;
   last_samples->has_parent_data = true;
@@ -579,7 +579,7 @@ colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *
     cvm::error("User required histogram with zero output frequency");
   }
 
-  grid   = new colvar_grid_count    (colvars);
+  grid = new colvar_grid_count(colvars);
   bin.assign(colvars.size(), 0);
 
   cvm::log("Finished histogram setup.\n");
@@ -588,7 +588,8 @@ colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *
 /// Destructor
 colvarbias_histogram::~colvarbias_histogram()
 {
-  if (grid_os.is_open())	grid_os.close();
+  if (grid_os.is_open())
+    grid_os.close();
 
   if (grid) {
     delete grid;

lib/colvars/colvarbias_meta.cpp

@@ -86,7 +86,7 @@ colvarbias_meta::colvarbias_meta(std::string const &conf, char const *key)
       colvars[i]->enable(colvar::task_grid);
     }
 
-    hills_energy           = new colvar_grid_scalar   (colvars);
+    hills_energy           = new colvar_grid_scalar(colvars);
     hills_energy_gradients = new colvar_grid_gradient(colvars);
   } else {
     rebin_grids = false;
@@ -959,7 +959,7 @@ void colvarbias_meta::update_replicas_registry()
         (replicas.back())->comm = multiple_replicas;
 
         if (use_grids) {
-          (replicas.back())->hills_energy           = new colvar_grid_scalar   (colvars);
+          (replicas.back())->hills_energy           = new colvar_grid_scalar(colvars);
           (replicas.back())->hills_energy_gradients = new colvar_grid_gradient(colvars);
         }
       }

lib/colvars/colvarcomp.h

@@ -1139,6 +1139,8 @@ class colvar::cartesian
 protected:
   /// Atom group
   cvm::atom_group atoms;
+  /// Which Cartesian coordinates to include
+  std::vector<size_t> axes;
 public:
   cartesian(std::string const &conf);
   cartesian();

lib/colvars/colvarcomp_distances.cpp

@@ -1296,17 +1296,40 @@ colvar::cartesian::cartesian(std::string const &conf)
   parse_group(conf, "atoms", atoms);
   atom_groups.push_back(&atoms);
 
+  bool use_x, use_y, use_z;
+  get_keyval(conf, "useX", use_x, true);
+  get_keyval(conf, "useY", use_y, true);
+  get_keyval(conf, "useZ", use_z, true);
+
+  axes.clear();
+  if (use_x) axes.push_back(0);
+  if (use_y) axes.push_back(1);
+  if (use_z) axes.push_back(2);
+
+  if (axes.size() == 0) {
+    cvm::error("Error: a \"cartesian\" component was defined with all three axes disabled.\n");
+  }
+
   x.type(colvarvalue::type_vector);
-  x.vector1d_value.resize(atoms.size() * 3);
+  x.vector1d_value.resize(atoms.size() * axes.size());
 }
 
 
 void colvar::cartesian::calc_value()
 {
-  int ia, j;
+  size_t const dim = axes.size();
+  size_t ia, j;
   for (ia = 0; ia < atoms.size(); ia++) {
-    for (j = 0; j < 3; j++) {
-      x.vector1d_value[3*ia + j] = atoms[ia].pos[j];
+    for (j = 0; j < dim; j++) {
+      x.vector1d_value[dim*ia + j] = atoms[ia].pos[axes[j]];
+    }
+  }
+
+  if (atoms.weights.size()) {
+    for (ia = 0; ia < atoms.size(); ia++) {
+      for (j = 0; j < dim; j++) {
+        x.vector1d_value[dim*ia + j] *= atoms.weights[ia];
+      }
     }
   }
 }
@@ -1322,14 +1345,24 @@ void colvar::cartesian::calc_gradients()
 
 void colvar::cartesian::apply_force(colvarvalue const &force)
 {
-  int ia, j;
+  size_t const dim = axes.size();
+  size_t ia, j;
   if (!atoms.noforce) {
     cvm::rvector f;
-    for (ia = 0; ia < atoms.size(); ia++) {
-      for (j = 0; j < 3; j++) {
-        f[j] = force.vector1d_value[3*ia + j];
+    if (atoms.weights.size()) {
+      for (ia = 0; ia < atoms.size(); ia++) {
+        for (j = 0; j < dim; j++) {
+          f[axes[j]] = force.vector1d_value[dim*ia + j];
+        }
+        atoms[ia].apply_force(f);
+      }
+    } else {
+      for (ia = 0; ia < atoms.size(); ia++) {
+        for (j = 0; j < dim; j++) {
+          f[axes[j]] = force.vector1d_value[dim*ia + j] / atoms.weights[ia];
+        }
+        atoms[ia].apply_force(f);
       }
-      atoms[ia].apply_force(f);
     }
   }
 }

lib/colvars/colvarparse.cpp

@@ -482,16 +482,6 @@ bool colvarparse::key_lookup(std::string const &conf,
     }
   }
 
-  // check it is not between quotes
-  //   if ( (conf.find_last_of  ("\"",
-  //                             conf.find_last_of  (white_space, pos)) !=
-  //         std::string::npos) &&
-  //        (conf.find_first_of ("\"",
-  //                             conf.find_first_of (white_space, pos)) !=
-  //         std::string::npos) )
-  //     return false;
-
-
   // save the pointer for a future call (when iterating over multiple
   // valid instances of the same keyword)
   save_pos = pos + key.size();
@@ -499,7 +489,7 @@ bool colvarparse::key_lookup(std::string const &conf,
   // get the remainder of the line
   size_t pl = conf.rfind("\n", pos);
   size_t line_begin = (pl == std::string::npos) ? 0 : pos;
-  size_t nl = conf.find  ("\n", pos);
+  size_t nl = conf.find("\n", pos);
   size_t line_end = (nl == std::string::npos) ? conf.size() : nl;
   std::string line(conf, line_begin, (line_end-line_begin));
 
@@ -569,7 +559,7 @@ bool colvarparse::key_lookup(std::string const &conf,
 
     if (data.size() && save_delimiters) {
       data_begin_pos.push_back(conf.find(data, pos+key.size()));
-      data_end_pos.push_back   (data_begin_pos.back()+data.size());
+      data_end_pos.push_back(data_begin_pos.back()+data.size());
       //       std::cerr << "key = " << key << ", data = \""
       //                 << data << "\", data_begin, data_end = "
       //                 << data_begin_pos.back() << ", " << data_end_pos.back()