git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11969 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/colvars/colvar.cpp

@@ -591,11 +591,12 @@ void colvar::enable (colvar::task const &t)
     }
     break;
 
-
   case task_output_value:
   case task_runave:
   case task_corrfunc:
   case task_ntot:
+  case task_langevin:
+  case task_output_energy:
     break;
 
   case task_gradients:
@@ -612,6 +613,7 @@ void colvar::enable (colvar::task const &t)
       build_atom_list();
     }
     break;
+
   }
 
 
@@ -660,6 +662,9 @@ void colvar::disable (colvar::task const &t)
   case task_lower_wall:
   case task_upper_wall:
   case task_ntot:
+  case task_langevin:
+  case task_output_energy:
+  case task_collect_gradients:
     break;
   }
 

lib/colvars/colvaratoms.cpp

@@ -14,8 +14,8 @@
 cvm::atom_group::atom_group (std::string const &conf,
                              char const        *key)
   : b_center (false), b_rotate (false), b_user_defined_fit (false),
-    ref_pos_group (NULL),
     b_fit_gradients (false),
+    ref_pos_group (NULL),
     noforce (false)
 {
   cvm::log ("Defining atom group \""+
@@ -27,7 +27,7 @@ cvm::atom_group::atom_group (std::string const &conf,
 
 cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
   : b_dummy (false), b_center (false), b_rotate (false),
-    ref_pos_group (NULL), b_fit_gradients (false),
+    b_fit_gradients (false), ref_pos_group (NULL),
     noforce (false)
 {
   this->reserve (atoms.size());
@@ -44,7 +44,7 @@ cvm::atom_group::atom_group (std::vector<cvm::atom> const &atoms)
 
 cvm::atom_group::atom_group()
   : b_dummy (false), b_center (false), b_rotate (false),
-    ref_pos_group (NULL), b_fit_gradients (false),
+    b_fit_gradients (false), ref_pos_group (NULL),
     noforce (false)
 {
   total_mass = 0.0;

lib/colvars/colvarbias.cpp

@@ -121,8 +121,8 @@ std::ostream & colvarbias::write_traj (std::ostream &os)
 colvarbias_harmonic::colvarbias_harmonic (std::string const &conf,
                                           char const *key)
   : colvarbias (conf, key),
-    target_nsteps (0),
+    target_nstages (0),
-    target_nstages (0)
+    target_nsteps (0)
 {
   get_keyval (conf, "forceConstant", force_k, 1.0);
   for (size_t i = 0; i < colvars.size(); i++) {

lib/colvars/colvarbias_meta.cpp

@@ -25,16 +25,16 @@
 
 colvarbias_meta::colvarbias_meta()
   : colvarbias(),
-    state_file_step (0),
+    new_hills_begin (hills.end()),
-    new_hills_begin (hills.end())
+    state_file_step (0)
 {
 }
 
 
 colvarbias_meta::colvarbias_meta (std::string const &conf, char const *key)
   : colvarbias (conf, key),
-    state_file_step (0),
+    new_hills_begin (hills.end()),
-    new_hills_begin (hills.end())
+    state_file_step (0)
 {
   if (cvm::n_abf_biases > 0)
     cvm::log ("Warning: running ABF and metadynamics together is not recommended unless applyBias is off for ABF.\n");

lib/colvars/colvarcomp.cpp

@@ -8,18 +8,18 @@
 colvar::cvc::cvc()
   : sup_coeff (1.0), sup_np (1),
     b_periodic (false),
-    b_debug_gradients (false),
     b_inverse_gradients (false),
-    b_Jacobian_derivative (false)
+    b_Jacobian_derivative (false),
+    b_debug_gradients (false)
 {}
 
 
 colvar::cvc::cvc (std::string const &conf)
   : sup_coeff (1.0), sup_np (1),
     b_periodic (false),
-    b_debug_gradients (false),
     b_inverse_gradients (false),
-    b_Jacobian_derivative (false)
+    b_Jacobian_derivative (false),
+    b_debug_gradients (false)
 {
   if (cvm::debug())
     cvm::log ("Initializing cvc base object.\n");

lib/colvars/colvargrid.h

@@ -173,19 +173,19 @@ public:
   /// \brief "Almost copy-constructor": only copies configuration
   /// parameters from another grid, but doesn't reallocate stuff;
   /// create() must be called after that;
-  colvar_grid (colvar_grid<T> const &g) : has_data (false),
+  colvar_grid (colvar_grid<T> const &g) : nd (g.nd),
-                                          nd (g.nd),
                                           nx (g.nx),
                                           mult (g.mult),
+                                          data(),
                                           cv (g.cv),
+                                          actual_value (g.actual_value),
                                           lower_boundaries (g.lower_boundaries),
                                           upper_boundaries (g.upper_boundaries),
+                                          periodic (g.periodic),
                                           hard_lower_boundaries (g.hard_lower_boundaries),
                                           hard_upper_boundaries (g.hard_upper_boundaries),
-                                          periodic (g.periodic),
                                           widths (g.widths),
-                                          actual_value (g.actual_value),
+                                          has_data (false)
-                                          data()
   {
     save_delimiters = false;
   }

lib/colvars/colvarmodule.cpp

@@ -815,6 +815,41 @@ void cvm::read_index_file (char const *filename)
 
 }
 
+
+void cvm::load_atoms (char const *file_name,
+                             std::vector<cvm::atom> &atoms,
+                             std::string const &pdb_field,
+                             double const pdb_field_value)
+{
+  proxy->load_atoms (file_name, atoms, pdb_field, pdb_field_value);
+}
+
+void cvm::load_coords (char const *file_name,
+                              std::vector<cvm::atom_pos> &pos,
+                              const std::vector<int> &indices,
+                              std::string const &pdb_field,
+                              double const pdb_field_value)
+{
+  // Differentiate between PDB and XYZ files
+  // for XYZ files, use CVM internal parser
+  // otherwise call proxy function for PDB
+
+  std::string const ext (strlen(file_name) > 4 ? (file_name + (strlen(file_name) - 4)) : file_name);
+  if (colvarparse::to_lower_cppstr (ext) == std::string (".xyz")) {
+    if ( pdb_field.size() > 0 ) {
+      cvm::fatal_error ("Error: PDB column may not be specified for XYZ coordinate file.\n");
+    }
+    cvm::load_coords_xyz (file_name, pos, indices);
+  } else {
+    proxy->load_coords (file_name, pos, indices, pdb_field, pdb_field_value);
+  }
+}
+
+void cvm::backup_file (char const *filename)
+{
+  proxy->backup_file (filename);
+}
+
 void cvm::load_coords_xyz (char const *filename,
                            std::vector<atom_pos> &pos,
                            const std::vector<int> &indices)

lib/colvars/colvarmodule.h

@@ -2,7 +2,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2013-12-13"
+#define COLVARS_VERSION "2014-05-08"
 #endif
 
 #ifndef COLVARS_DEBUG
@@ -483,40 +483,6 @@ inline cvm::real cvm::position_dist2 (cvm::atom_pos const &pos1,
   return proxy->position_dist2 (pos1, pos2);
 }
 
-inline void cvm::load_atoms (char const *file_name,
-                             std::vector<cvm::atom> &atoms,
-                             std::string const &pdb_field,
-                             double const pdb_field_value)
-{
-  proxy->load_atoms (file_name, atoms, pdb_field, pdb_field_value);
-}
-
-inline void cvm::load_coords (char const *file_name,
-                              std::vector<cvm::atom_pos> &pos,
-                              const std::vector<int> &indices,
-                              std::string const &pdb_field,
-                              double const pdb_field_value)
-{
-  // Differentiate between PDB and XYZ files
-  // for XYZ files, use CVM internal parser
-  // otherwise call proxy function for PDB
-
-  char const *ext = strlen(file_name) > 4 ? file_name + (strlen(file_name) - 4) : file_name;
-  if ( !strncmp(ext, ".xyz", 4) || !strncmp(ext, ".XYZ", 4) ) {
-    if ( pdb_field.size() > 0 ) {
-      cvm::fatal_error ("Error: PDB column may not be specified for XYZ coordinate file.\n");
-    }
-    cvm::load_coords_xyz (file_name, pos, indices);
-  } else {
-    proxy->load_coords (file_name, pos, indices, pdb_field, pdb_field_value);
-  }
-}
-
-inline void cvm::backup_file (char const *filename)
-{
-  proxy->backup_file (filename);
-}
-
 inline cvm::real cvm::rand_gaussian (void)
 {
   return proxy->rand_gaussian();

lib/colvars/colvarparse.cpp

@@ -595,7 +595,7 @@ std::istream & operator>> (std::istream &is, colvarparse::read_block const &rb)
   size_t brace_count = 1;
   std::string line;
   while (colvarparse::getline_nocomments (is, line)) {
-    size_t br = 0, br_old;
+    size_t br = 0, br_old = 0;
     while ( (br = line.find_first_of ("{}", br)) != std::string::npos) {
       if (line[br] == '{') brace_count++;
       if (line[br] == '}') brace_count--;