more changes to support late initialization of masses

lib/colvars/colvar.cpp

@@ -669,9 +669,12 @@ void colvar::disable (colvar::task const &t)
 
 void colvar::setup() {
   // loop over all components to reset masses of all groups
-  for (std::vector<cvc *>::iterator cci = cvcs.begin();
-       cci != cvcs.end(); cci++) {
-    (*cci)->setup();
+  for (size_t i = 0; i < cvcs.size(); i++) {
+    for (size_t ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
+      cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
+      atoms.read_positions();
+      atoms.reset_mass();
+    }
   }
 }
 

lib/colvars/colvarcomp.cpp

@@ -55,16 +55,6 @@ void colvar::cvc::parse_group (std::string const &conf,
 }
 
 
-void colvar::cvc::setup()
-{
-  // loop over all atom groups to reset their masses
-  for (std::vector<cvm::atom_group *>::iterator agi = atom_groups.begin();
-       agi != atom_groups.end();  agi++) {
-    (*agi)->reset_mass();
-  }
-}
-
-
 colvar::cvc::~cvc()
 {}
 

lib/colvars/colvarcomp.h

@@ -113,10 +113,6 @@ public:
   /// objects are declared within other ones)
   cvc();
 
-  /// \brief Reinitialize internal data for MD codes that
-  /// can change parameters between runs
-  void setup();
-
   /// Destructor
   virtual ~cvc();
 

lib/colvars/colvarmodule.h

@@ -2,7 +2,7 @@
 #define COLVARMODULE_H
 
 #ifndef COLVARS_VERSION
-#define COLVARS_VERSION "2013-06-18"
+#define COLVARS_VERSION "2013-06-19"
 #endif
 
 #ifndef COLVARS_DEBUG

src/USER-COLVARS/colvarproxy_lammps.cpp

@@ -97,12 +97,11 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
 }
 
 
-void colvarproxy_lammps::init(const char *conf_file, const int *typemap)
+void colvarproxy_lammps::init(const char *conf_file)
 {
-  _typemap = typemap;
-
   // create the colvarmodule instance
   colvars = new colvarmodule(conf_file,this);
+  cvm::log ("Notice! Postponing initializing of masses.\n");
 
   if (_lmp->update->ntimestep != 0) {
     cvm::log ("Initializing step number as firstTimestep.\n");
@@ -117,9 +116,6 @@ void colvarproxy_lammps::init(const char *conf_file, const int *typemap)
     log(cvm::line_marker);
     log("Info: done initializing the colvars proxy object.\n");
   }
-
-  // this is only valid in this function.
-  _typemap = NULL;
 }
 
 colvarproxy_lammps::~colvarproxy_lammps()
@@ -132,6 +128,12 @@ colvarproxy_lammps::~colvarproxy_lammps()
   }
 }
 
+// re-initialize data where needed
+void colvarproxy_lammps::setup()
+{
+  colvars->setup();
+}
+
 // trigger colvars computation
 double colvarproxy_lammps::compute()
 {
@@ -338,7 +340,7 @@ void colvarproxy_lammps::backup_file(char const *filename)
 int colvarproxy_lammps::init_lammps_atom(const int &aid, cvm::atom *atom)
 {
   atom->id = aid;
-  atom->mass = _lmp->atom->mass[_typemap[aid]];
+  atom->mass = 0.0;
 
   for (size_t i = 0; i < colvars_atoms.size(); i++) {
     if (colvars_atoms[i] == aid) {
@@ -353,7 +355,7 @@ int colvarproxy_lammps::init_lammps_atom(const int &aid, cvm::atom *atom)
   colvars_atoms.push_back(aid);
   struct commdata c;
   c.tag = aid;
-  c.type = _typemap[aid];
+  c.type = 0;
   c.x = c.y = c.z = 0.0;
   positions.push_back(c);
   total_forces.push_back(c);
@@ -422,13 +424,13 @@ cvm::atom::~atom()
   }
 }
 
-
 void cvm::atom::read_position()
 {
   colvarproxy_lammps const * const cp = (colvarproxy_lammps *) cvm::proxy;
   this->pos.x = cp->positions[this->index].x;
   this->pos.y = cp->positions[this->index].y;
   this->pos.z = cp->positions[this->index].z;
+  this->mass = cp->positions[this->index].m;
 }
 
 void cvm::atom::read_velocity()

src/USER-COLVARS/colvarproxy_lammps.h

@@ -17,7 +17,7 @@
 /* struct for packed data communication of coordinates and forces. */
 struct commdata {
   int tag,type;
-  double x,y,z;
+    double x,y,z,m;
 };
 
 inline std::ostream & operator<< (std::ostream &out, const commdata &cd)
@@ -38,9 +38,6 @@ class colvarproxy_lammps : public colvarproxy {
   class LAMMPS_NS::LAMMPS *_lmp;
   class LAMMPS_NS::RanPark *_random;
 
-  // pointers to LAMMPS provided storage
-  const int *_typemap;
-
   // state of LAMMPS properties
   double t_target;
   double bias_energy;
@@ -66,7 +63,8 @@ class colvarproxy_lammps : public colvarproxy {
   colvarproxy_lammps (LAMMPS_NS::LAMMPS *lmp, const char *,
                       const char *, const int, const double);
   virtual ~colvarproxy_lammps();
-  void init(const char*, const int *);
+  void init(const char*);
+  void setup();
 
  // disable default and copy constructor
  private:

src/USER-COLVARS/fix_colvars.cpp

@@ -293,9 +293,6 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
   if (narg < 4)
     error->all(FLERR,"Illegal fix colvars command: too few arguments");
 
-  if (atom->rmass_flag)
-    error->all(FLERR,"Cannot use fix colvars for atoms with rmass attribute");
-
   if (instances > 0)
     error->all(FLERR,"Only one colvars fix can be active at a time");
   ++instances;
@@ -420,7 +417,6 @@ void FixColvars::init()
 
 void FixColvars::setup(int vflag)
 {
-  int *typemap,*type_buf;
   const int * const tag  = atom->tag;
   const int * const type = atom->type;
   int i,nme,tmp,ndata,nlocal_max,tag_max,max;
@@ -433,6 +429,8 @@ void FixColvars::setup(int vflag)
   if (init_flag == 0) {
     init_flag = 1;
 
+#if 0
+
     // collect a list of atom type by atom id for the entire system.
     // the colvar module requires this information to set masses. :-(
 
@@ -478,6 +476,7 @@ void FixColvars::setup(int vflag)
       MPI_Rsend(type_buf, nme, MPI_INT, 0, 0, world);
     }
     delete type_buf;
+#endif
 
     // now create and initialize the colvars proxy
 
@@ -505,13 +504,11 @@ void FixColvars::setup(int vflag)
       }
 
       proxy = new colvarproxy_lammps(lmp,inp_name,out_name,rng_seed,t_target);
-      proxy->init(conf_file,typemap);
+      proxy->init(conf_file);
       coords = proxy->get_coords();
       forces = proxy->get_forces();
       oforce = proxy->get_oforce();
       num_coords = coords->size();
-
-      delete typemap;
     }
 
     // send the list of all colvar atom IDs to all nodes.
@@ -585,6 +582,11 @@ void FixColvars::setup(int vflag)
           cd[i].y = x[k][1];
           cd[i].z = x[k][2];
         }
+        if (atom->rmass_flag) {
+          cd[i].m = atom->rmass[k];
+        } else {
+          cd[i].m = atom->mass[type[k]];
+        }
       }
     }
 
@@ -606,6 +608,7 @@ void FixColvars::setup(int vflag)
           cd[j].x = comm_buf[k].x;
           cd[j].y = comm_buf[k].y;
           cd[j].z = comm_buf[k].z;
+          cd[j].m = comm_buf[k].m;
           of[j].x = of[j].y = of[j].z = 0.0;
         }
       }
@@ -636,6 +639,12 @@ void FixColvars::setup(int vflag)
           comm_buf[nme].z = x[k][2];
         }
 
+        if (atom->rmass_flag) {
+          comm_buf[nme].m = atom->rmass[k];
+        } else {
+          comm_buf[nme].m = atom->mass[type[k]];
+        }
+
         ++nme;
       }
     }
@@ -644,6 +653,9 @@ void FixColvars::setup(int vflag)
     MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
   }
 
+  // run pre-run setup in colvarproxy
+  proxy->setup();
+
   // initialize forces
   if (strstr(update->integrate_style,"verlet") || (update->whichflag == 2))
     post_force(vflag);