--- trunk/mdtools/md_code/InitializeFromFile.cpp	2002/07/09 18:40:59	11
+++ trunk/mdtools/md_code/InitializeFromFile.cpp	2002/12/12 21:21:59	206
@@ -9,37 +9,62 @@
 #include <sys/stat.h>
 
 #include "ReadWrite.hpp"
+#include "simError.h"
 
 
 InitializeFromFile :: InitializeFromFile( char *in_name ){
+#ifdef IS_MPI
+  if (worldRank == 0) {
+#endif
 
   c_in_file = fopen(in_name, "r");
   if(c_in_file == NULL){
-    printf("Cannot open file: %s\n", in_name);
-    exit(8);
+    sprintf(painCave.errMsg,
+	    "Cannot open file: %s\n", in_name);
+    painCave.isFatal = 1;
+    simError();
   }
   
   strcpy( c_in_name, in_name);
+#ifdef IS_MPI
+  }
+ strcpy( checkPointMsg, "Infile opened for reading successfully." );
+  MPIcheckPoint();
+#endif
   return;  
 }
 
 InitializeFromFile :: ~InitializeFromFile( ){
-  
+#ifdef IS_MPI
+  if (worldRank == 0) {
+#endif
   int error;
   error = fclose( c_in_file );
   if( error ){
-    fprintf( stderr, "Error closing %s\n", c_in_name );
+    sprintf( painCave.errMsg,
+	     "Error closing %s\n", c_in_name );
+    simError();
   }
+#ifdef IS_MPI
+  }
+  strcpy( checkPointMsg, "Infile closed successfully." );
+  MPIcheckPoint();
+#endif
+
   return;
 }
 
 
-void InitializeFromFile :: read_xyz( SimInfo* entry_plug ){
+void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
 
   int i; // loop counter
 
   int n_atoms; // the number of atoms
   char read_buffer[2000]; //the line buffer for reading 
+#ifdef IS_MPI
+  char send_buffer[2000];
+#endif
+
   char *eof_test; // ptr to see when we reach the end of the file 
   char *foo; // the pointer to the current string token 
 
@@ -49,6 +74,10 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
   double jx, jy, jz; // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
 
+  entry_plug = the_entry_plug
+
+
+#ifndef IS_MPI
   eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
   if( eof_test == NULL ){
     std::cerr << "error reading 1st line of" << c_in_name << "\n";
@@ -60,30 +89,35 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
   DirectionalAtom* dAtom;
 
   if( n_atoms != entry_plug->n_atoms ){
-    fprintf( stderr,
+    sprintf( painCave.errMsg,
 	     "Initialize from File error. %s n_atoms, %d, "
 	     "does not match the BASS file's n_atoms, %d.\n",
 	     c_in_name, n_atoms, entry_plug->n_atoms );
-    exit(8);
+    painCave.isFatal = 1;
+    simError();
   }
   
   //read and toss the comment line 
   
   eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
   if(eof_test == NULL){
-    printf("error in reading commment in %s\n", c_in_name);
-    exit(8);
+    sprintf( painCave.errMsg,
+	     "error in reading commment in %s\n", c_in_name);
+    painCave.isFatal = 1;
+    simError();
   }
 
   for( i=0; i < n_atoms; i++){
     
     eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
     if(eof_test == NULL){
-      printf("error in reading file %s\n"
-	     "natoms  = %d; index = %d\n"
-	     "error reading the line from the file.\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf(painCave.errMsg,
+	      "error in reading file %s\n"
+	      "natoms  = %d; index = %d\n"
+	      "error reading the line from the file.\n",
+	      c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
 
     foo = strtok(read_buffer, " ,;\t");
@@ -91,40 +125,47 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
     // check the atom name to the current atom
 
     if( strcmp( foo, atoms[i]->getType() ) ){
-      fprintf( stderr,
+      sprintf( painCave.errMsg,
 	       "Initialize from file error. Atom %s at index %d "
 	       "in file %s does not"
 	       " match the BASS atom %s.\n",
 	       foo, i, c_in_name, atoms[i]->getType() );
-      exit(8);
+      painCave.isFatal = 1;
+      simError();
     }
     
     // get the positions
 
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      printf("error in reading postition x from %s\n"
-	     "natoms  = %d, index = %d\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "error in reading postition x from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
     (void)sscanf( foo, "%lf", &rx );
    
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      printf("error in reading postition y from %s\n"
-	     "natoms  = %d, index = %d\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "error in reading postition y from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
     (void)sscanf( foo, "%lf", &ry );
      
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      printf("error in reading postition z from %s\n"
-	     "natoms  = %d, index = %d\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "error in reading postition z from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
     (void)sscanf( foo, "%lf", &rz );
     
@@ -132,28 +173,34 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
 
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      printf("error in reading velocity x from %s\n"
-	     "natoms  = %d, index = %d\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "error in reading velocity x from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
     (void)sscanf( foo, "%lf", &vx );
     
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      printf("error in reading velocity y from %s\n"
-	     "natoms  = %d, index = %d\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "error in reading velocity y from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
     (void)sscanf( foo, "%lf", &vy );
     
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
-      printf("error in reading velocity z from %s\n"
-	     "natoms  = %d, index = %d\n",
-	     c_in_name, n_atoms, i );
-      exit(8);
+      sprintf( painCave.errMsg,
+	       "error in reading velocity z from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
     }
     (void)sscanf( foo, "%lf", &vz );
     
@@ -164,37 +211,45 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
       
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading quaternion 0 from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-	exit(8);
+	sprintf(painCave.errMsg,
+		"error in reading quaternion 0 from %s\n"
+		"natoms  = %d, index = %d\n",
+		c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
       (void)sscanf( foo, "%lf", &q[0] );
       
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading quaternion 1 from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-	exit(8);
+	sprintf( painCave.errMsg,
+		 "error in reading quaternion 1 from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
       (void)sscanf( foo, "%lf", &q[1] );
       
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading quaternion 2 from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-	exit(8);
+	sprintf( painCave.errMsg,
+		 "error in reading quaternion 2 from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
       (void)sscanf( foo, "%lf", &q[2] );
-
+      
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading quaternion 3 from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-	exit(8);
+	sprintf( painCave.errMsg,
+		 "error in reading quaternion 3 from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
       (void)sscanf( foo, "%lf", &q[3] );
       
@@ -202,29 +257,289 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
       
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading angular momentum jx from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-	exit(8);
+	sprintf( painCave.errMsg,
+		 "error in reading angular momentum jx from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
       (void)sscanf( foo, "%lf", &jx );
       
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading angular momentum jy from %s\n"
-	       "natoms  = %d, index = %d\n",
-	       c_in_name, n_atoms, i );
-	exit(8);
+	sprintf( painCave.errMsg,
+		 "error in reading angular momentum jy from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
       (void)sscanf( foo, "%lf", &jy );
       
       foo = strtok(NULL, " ,;\t");
       if(foo == NULL){
-	printf("error in reading angular momentum jz from %s\n"
+	sprintf( painCave.errMsg,
+		 "error in reading angular momentum jz from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
+      (void)sscanf( foo, "%lf", &jz );
+      
+      dAtom = ( DirectionalAtom* )atoms[i];
+
+      // check that the quaternion vector is normalized
+
+      qSqr = (q[0] * q[0]) + (q[1] * q[1]) + (q[2] * q[2]) + (q[3] * q[3]);
+      
+      qLength = sqrt( qSqr );
+      q[0] = q[0] / qLength;
+      q[1] = q[1] / qLength;
+      q[2] = q[2] / qLength;
+      q[3] = q[3] / qLength;
+      
+      dAtom->setQ( q );
+      
+      // add the angular velocities
+
+      dAtom->setJx( jx );
+      dAtom->setJy( jy );
+      dAtom->setJz( jz );
+    }
+    
+    // add the positions and velocities to the atom
+    
+    atoms[i]->setX( rx );
+    atoms[i]->setY( ry );
+    atoms[i]->setZ( rz );
+    
+    atoms[i]->set_vx( vx );
+    atoms[i]->set_vy( vy );
+    atoms[i]->set_vz( vz );
+    
+  }
+
+
+  // MPI Section of code..........
+#else //IS_MPI
+
+
+
+
+  if (worldRank == 0) {
+    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
+    if( eof_test == NULL ){
+      sprintf( painCave.errMsg,
+	       "Error reading 1st line of %d \n ",c_in_name);
+      painCave.isFatal = 1;
+      simError();
+    }
+    
+    (void)sscanf(read_buffer, "%d", &n_atoms);
+    
+    Atom **atoms = entry_plug->atoms;
+    DirectionalAtom* dAtom;
+    
+    if( n_atoms != entry_plug->n_atoms ){
+      sprintf( painCave.errMsg,
+	       "Initialize from File error. %s n_atoms, %d, "
+	       "does not match the BASS file's n_atoms, %d.\n",
+	       c_in_name, n_atoms, entry_plug->n_atoms );
+      painCave.isFatal = 1;
+      simError();
+    }
+    
+    //read and toss the comment line 
+    
+    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
+    if(eof_test == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading commment in %s\n", c_in_name);
+      painCave.isFatal = 1;
+      simError();
+    }
+  }
+  for( i=0; i < n_atoms; i++){
+    
+    eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
+    if(eof_test == NULL){
+      sprintf(painCave.errMsg,
+	      "error in reading file %s\n"
+	      "natoms  = %d; index = %d\n"
+	      "error reading the line from the file.\n",
+	      c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
+    }
+
+    foo = strtok(read_buffer, " ,;\t");
+    
+    // check the atom name to the current atom
+
+    if( strcmp( foo, atoms[i]->getType() ) ){
+      sprintf( painCave.errMsg,
+	       "Initialize from file error. Atom %s at index %d "
+	       "in file %s does not"
+	       " match the BASS atom %s.\n",
+	       foo, i, c_in_name, atoms[i]->getType() );
+      painCave.isFatal = 1;
+      simError();
+    }
+    
+    // get the positions
+
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading postition x from %s\n"
 	       "natoms  = %d, index = %d\n",
 	       c_in_name, n_atoms, i );
-	exit(8);
+      painCave.isFatal = 1;
+      simError();
+    }
+    (void)sscanf( foo, "%lf", &rx );
+   
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading postition y from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
+    }
+    (void)sscanf( foo, "%lf", &ry );
+     
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading postition z from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
+    }
+    (void)sscanf( foo, "%lf", &rz );
+    
+    // get the velocities
+
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading velocity x from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
+    }
+    (void)sscanf( foo, "%lf", &vx );
+    
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading velocity y from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
+    }
+    (void)sscanf( foo, "%lf", &vy );
+    
+    foo = strtok(NULL, " ,;\t");
+    if(foo == NULL){
+      sprintf( painCave.errMsg,
+	       "error in reading velocity z from %s\n"
+	       "natoms  = %d, index = %d\n",
+	       c_in_name, n_atoms, i );
+      painCave.isFatal = 1;
+      simError();
+    }
+    (void)sscanf( foo, "%lf", &vz );
+    
+    
+    // get the quaternions
+    
+    if( atoms[i]->isDirectional() ){
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf(painCave.errMsg,
+		"error in reading quaternion 0 from %s\n"
+		"natoms  = %d, index = %d\n",
+		c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
       }
+      (void)sscanf( foo, "%lf", &q[0] );
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "error in reading quaternion 1 from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
+      (void)sscanf( foo, "%lf", &q[1] );
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "error in reading quaternion 2 from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
+      (void)sscanf( foo, "%lf", &q[2] );
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "error in reading quaternion 3 from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
+      (void)sscanf( foo, "%lf", &q[3] );
+      
+      // get the angular velocities
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "error in reading angular momentum jx from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
+      (void)sscanf( foo, "%lf", &jx );
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "error in reading angular momentum jy from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
+      (void)sscanf( foo, "%lf", &jy );
+      
+      foo = strtok(NULL, " ,;\t");
+      if(foo == NULL){
+	sprintf( painCave.errMsg,
+		 "error in reading angular momentum jz from %s\n"
+		 "natoms  = %d, index = %d\n",
+		 c_in_name, n_atoms, i );
+	painCave.isFatal = 1;
+	simError();
+      }
       (void)sscanf( foo, "%lf", &jz );
       
       dAtom = ( DirectionalAtom* )atoms[i];
@@ -259,4 +574,7 @@ void InitializeFromFile :: read_xyz( SimInfo* entry_pl
     atoms[i]->set_vz( vz );
     
   }
+#endif
 }
+
+char* IntitializeFromFile::parseDumpLine(char* readLine);