git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-COLVARS/colvarproxy_lammps.cpp

@@ -2,7 +2,6 @@
 #include "mpi.h"
 #include "lammps.h"
 #include "atom.h"
-#include "comm.h"
 #include "error.h"
 #include "output.h"
 #include "random_park.h"
@@ -62,8 +61,9 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
                                        const char *inp_name,
                                        const char *out_name,
                                        const int seed,
-                                       const double temp)
-  : _lmp(lmp)
+                                       const double temp,
+                                       MPI_Comm root2root)
+  : _lmp(lmp), inter_comm(root2root)
 {
   if (cvm::debug())
     log("Initializing the colvars proxy object.\n");
@@ -90,7 +90,7 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
   // output prefix is always given
   output_prefix_str = std::string(out_name);
   // not so for restarts
-  restart_prefix_str = std::string("rest");
+  restart_output_prefix_str = std::string("rest");
 
   // check if it is possible to save output configuration
   if ((!output_prefix_str.size()) && (!restart_output_prefix_str.size())) {
@@ -101,13 +101,19 @@ colvarproxy_lammps::colvarproxy_lammps(LAMMPS_NS::LAMMPS *lmp,
   // try to extract a restart prefix from a potential restart command.
   LAMMPS_NS::Output *outp = _lmp->output;
   if ((outp->restart_every_single > 0) && (outp->restart1 != 0)) {
-      restart_prefix_str = std::string(outp->restart1);
+      restart_output_prefix_str = std::string(outp->restart1);
   } else if  ((outp->restart_every_double > 0) && (outp->restart2a != 0)) {
-    restart_prefix_str = std::string(outp->restart2a);
+    restart_output_prefix_str = std::string(outp->restart2a);
   }
   // trim off unwanted stuff from the restart prefix
-  if (restart_prefix_str.rfind(".*") != std::string::npos)
-    restart_prefix_str.erase(restart_prefix_str.rfind(".*"),2);
+  if (restart_output_prefix_str.rfind(".*") != std::string::npos)
+    restart_output_prefix_str.erase(restart_output_prefix_str.rfind(".*"),2);
+
+  // initialize multi-replica support, if available
+  if (replica_enabled()) {
+    MPI_Comm_rank(inter_comm, &inter_me);
+    MPI_Comm_size(inter_comm, &inter_num);
+  }
 }
 
 
@@ -393,6 +399,36 @@ int colvarproxy_lammps::init_lammps_atom(const int &aid, cvm::atom *atom)
   return colvars_atoms.size()-1;
 }
 
+// multi-replica support
+
+void colvarproxy_lammps::replica_comm_barrier() {
+  MPI_Barrier(inter_comm);
+}
+
+int colvarproxy_lammps::replica_comm_recv(char* msg_data,
+                                          int buf_len, int src_rep)
+{
+  MPI_Status status;
+  int retval;
+
+  retval = MPI_Recv(msg_data,buf_len,MPI_CHAR,src_rep,0,inter_comm,&status);
+  if (retval == MPI_SUCCESS) {
+    MPI_Get_count(&status, MPI_CHAR, &retval);
+  } else retval = 0;
+  return retval;
+}
+
+int colvarproxy_lammps::replica_comm_send(char* msg_data,
+                                                  int msg_len, int dest_rep)
+{
+  int retval;
+  retval = MPI_Send(msg_data,msg_len,MPI_CHAR,dest_rep,0,inter_comm);
+  if (retval == MPI_SUCCESS) {
+    retval = msg_len;
+  } else retval = 0;
+  return retval;
+}
+
 // atom member functions, LAMMPS specific implementations
 
 cvm::atom::atom(const int &id)

src/USER-COLVARS/colvarproxy_lammps.h

@@ -44,10 +44,6 @@ class colvarproxy_lammps : public colvarproxy {
   int  restart_every;
   int  previous_step;
 
-  std::string input_prefix_str;
-  std::string output_prefix_str;
-  std::string restart_prefix_str;
-
   bool first_timestep;
   bool system_force_requested;
   bool do_exit;
@@ -59,10 +55,13 @@ class colvarproxy_lammps : public colvarproxy {
   std::vector<struct commdata> applied_forces;
   std::vector<struct commdata> previous_applied_forces;
 
+  MPI_Comm inter_comm;     // MPI comm with 1 root proc from each world
+  int inter_me, inter_num; // rank for the inter replica comm
+
  public:
   friend class cvm::atom;
   colvarproxy_lammps (LAMMPS_NS::LAMMPS *lmp, const char *,
-                      const char *, const int, const double);
+                      const char *, const int, const double, MPI_Comm);
   virtual ~colvarproxy_lammps();
   void init(const char*);
   void setup();
@@ -102,9 +101,6 @@ class colvarproxy_lammps : public colvarproxy {
   cvm::real temperature() { return t_target; };
   cvm::real dt() { return _lmp->update->dt * _lmp->force->femtosecond; };
 
-  inline std::string input_prefix() { return input_prefix_str; };
-  inline std::string output_prefix() { return output_prefix_str; };
-  inline std::string restart_output_prefix() { return restart_prefix_str; };
   inline size_t restart_frequency() { return restart_every; };
 
   void add_energy (cvm::real energy) { bias_energy = energy; };
@@ -137,6 +133,26 @@ class colvarproxy_lammps : public colvarproxy {
 
   cvm::real rand_gaussian(void) { return _random->gaussian(); };
 
+  // implementation of optional methods from base class
+ public:
+  // 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);
 };
 
 #endif

src/USER-COLVARS/fix_colvars.cpp

@@ -30,6 +30,7 @@
 #include "memory.h"
 #include "modify.h"
 #include "respa.h"
+#include "universe.h"
 #include "update.h"
 #include "citeme.h"
 
@@ -276,6 +277,7 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
   restart_global = 1;
 
   me = comm->me;
+  root2root = MPI_COMM_NULL;
 
   conf_file = strdup(arg[3]);
   rng_seed = 1966;
@@ -352,6 +354,9 @@ FixColvars::~FixColvars()
     delete hashtable;
   }
 
+  if (root2root != MPI_COMM_NULL)
+    MPI_Comm_free(&root2root);
+
   --instances;
 }
 
@@ -397,7 +402,14 @@ void FixColvars::one_time_init()
   if (init_flag) return;
   init_flag = 1;
 
-   // create and initialize the colvars proxy
+  if (universe->nworlds > 1) {
+    // create inter root communicator
+    int color = 1;
+    if (me == 0) color = 0;
+    MPI_Comm_split(universe->uworld,color,universe->iworld,&root2root);
+  }
+  
+  // create and initialize the colvars proxy
 
   if (me == 0) {
     if (screen) fputs("colvars: Creating proxy instance\n",screen);
@@ -428,7 +440,8 @@ void FixColvars::one_time_init()
       }
     }
 
-    proxy = new colvarproxy_lammps(lmp,inp_name,out_name,rng_seed,t_target);
+    proxy = new colvarproxy_lammps(lmp,inp_name,out_name,
+                                   rng_seed,t_target,root2root);
     proxy->init(conf_file);
     coords = proxy->get_coords();
     forces = proxy->get_forces();

src/USER-COLVARS/fix_colvars.h

@@ -84,6 +84,7 @@ class FixColvars : public Fix {
   int init_flag;       // 1 if initialized, 0 if not
   static  int instances; // count fix instances, since colvars currently
                          // only supports one instance at a time
+  MPI_Comm root2root;   // inter-root communicator for multi-replica support
   void one_time_init(); // one time initialization
 };
 

src/pair_hybrid.cpp

@@ -704,13 +704,10 @@ void PairHybrid::modify_params(int narg, char **arg)
 {
   if (narg == 0) error->all(FLERR,"Illegal pair_modify command");
 
-  // apply args to pair hybrid itself
-  // important for some keywords like tail or compute
-
-  Pair::modify_params(narg,arg);
-
   // if 1st keyword is pair, then apply args to one sub-style
   // else pass args to every sub-style
+  // also apply all args (except pair) to pair hybrid itself
+  //   important for some keywords like tail or compute
 
   if (strcmp(arg[0],"pair") == 0) {
     if (narg < 2) error->all(FLERR,"Illegal pair_modify command");
@@ -718,20 +715,24 @@ void PairHybrid::modify_params(int narg, char **arg)
     for (m = 0; m < nstyles; m++)
       if (strcmp(arg[1],keywords[m]) == 0) break;
     if (m == nstyles) error->all(FLERR,"Unknown pair_modify hybrid sub-style");
-    if (multiple[m] == 0)
+    if (multiple[m] == 0) {
+      Pair::modify_params(narg-2,&arg[2]);
       styles[m]->modify_params(narg-2,&arg[2]);
-    else {
+    } else {
       if (narg < 3) error->all(FLERR,"Illegal pair_modify command");
       int multiflag = force->inumeric(FLERR,arg[2]);
       for (m = 0; m < nstyles; m++)
         if (strcmp(arg[1],keywords[m]) == 0 && multiflag == multiple[m]) break;
       if (m == nstyles) 
         error->all(FLERR,"Unknown pair_modify hybrid sub-style");
+      Pair::modify_params(narg-2,&arg[3]);
       styles[m]->modify_params(narg-3,&arg[3]);
     }
     
-  } else 
+  } else {
+    Pair::modify_params(narg,arg);
     for (int m = 0; m < nstyles; m++) styles[m]->modify_params(narg,arg);
+  }
 }
 
 /* ----------------------------------------------------------------------