--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/10 22:15:53	590
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/08/12 19:56:49	689
@@ -26,7 +26,10 @@ using namespace initFile;
 
 #endif // is_mpi
 
-InitializeFromFile :: InitializeFromFile( char *in_name ){
+InitializeFromFile::InitializeFromFile( char *in_name ){
+
+  std::cerr << "Hello from Initialize from file.\n";
+
 #ifdef IS_MPI
   if (worldRank == 0) {
 #endif
@@ -48,7 +51,7 @@ InitializeFromFile :: InitializeFromFile( char *in_nam
   return;  
 }
 
-InitializeFromFile :: ~InitializeFromFile( ){
+InitializeFromFile::~InitializeFromFile( ){
 #ifdef IS_MPI
   if (worldRank == 0) {
 #endif
@@ -69,7 +72,7 @@ InitializeFromFile :: ~InitializeFromFile( ){
 }
 
 
-void InitializeFromFile :: read_xyz( SimInfo* the_simnfo ){
+void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
 
   int i, j, done, which_node, which_atom; // loop counter
 
@@ -83,6 +86,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
   char *eof_test; // ptr to see when we reach the end of the file 
   char *parseErr;
   int procIndex;
+  double currTime;
   double boxMat[9];
   double theBoxMat3[3][3];
 
@@ -123,7 +127,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     simError();
   }
 
-  parseErr = parseBoxLine( read_buffer, boxMat );
+  parseErr = parseBoxLine( read_buffer, boxMat, currTime );
   if( parseErr != NULL ){
     strcpy( painCave.errMsg, parseErr );
     painCave.isFatal = 1;
@@ -134,6 +138,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
 
   simnfo->setBoxM( theBoxMat3 );
+  simnfo->setTime( currTime );
 
 
   for( i=0; i < n_atoms; i++){
@@ -210,7 +215,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
       simError();
     }
     
-    parseErr = parseBoxLine( read_buffer, boxMat );
+    parseErr = parseBoxLine( read_buffer, boxMat, currTime );
     if( parseErr != NULL ){
       strcpy( painCave.errMsg, parseErr );
       haveError = 1;
@@ -218,6 +223,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     }
 
     MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD );
+    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD );
   
     if(haveError) nodeZeroError();
 
@@ -272,6 +278,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
   } else {
     
     MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD);
+    MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD);
 
     done = 0;
     while (!done) {
@@ -309,6 +316,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_simn
     for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i];
 
   simnfo->setBoxM( theBoxMat3 );
+  simnfo->setTime( currTime );
 
    
 #endif
@@ -318,8 +326,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 
   char *foo; // the pointer to the current string token 
   
-  double rx, ry, rz; // position place holders
-  double vx, vy, vz; // velocity placeholders
+  double pos[3]; // position place holders
+  double vel[3]; // velocity placeholders
   double q[4]; // the quaternions
   double jx, jy, jz; // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
@@ -372,7 +380,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  rx = atof( foo );
+  pos[0] = atof( foo );
    
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -382,7 +390,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  ry = atof( foo );
+  pos[1] = atof( foo );
      
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -392,7 +400,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  rz = atof( foo );    
+  pos[2] = atof( foo );    
 
 
   // get the velocities
@@ -405,7 +413,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vx = atof( foo );
+  vel[0] = atof( foo );
     
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -415,7 +423,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vy = atof( foo );
+  vel[1] = atof( foo );
     
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -425,7 +433,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vz = atof( foo );
+  vel[2] = atof( foo );
     
     
   // get the quaternions
@@ -527,19 +535,15 @@ char* InitializeFromFile::parseDumpLine(char* readLine
     
   // add the positions and velocities to the atom
     
-  atoms[atomIndex]->setX( rx );
-  atoms[atomIndex]->setY( ry );
-  atoms[atomIndex]->setZ( rz );
-    
-  atoms[atomIndex]->set_vx( vx );
-  atoms[atomIndex]->set_vy( vy );
-  atoms[atomIndex]->set_vz( vz );
+  atoms[atomIndex]->setPos( pos );
+  atoms[atomIndex]->setVel( vel );
 
   return NULL;
 }
 
 
-char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9]){
+char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9],
+				       double &time ){
 
   char *foo; // the pointer to the current string token 
   int j;
@@ -547,8 +551,15 @@ char* InitializeFromFile::parseBoxLine(char* readLine,
   // set the string tokenizer
   
   foo = strtok(readLine, " ,;\t");
-  // ignore the first token which is the time stamp.
+  // set the timeToken.
 
+  if(foo == NULL){
+    sprintf( painCave.errMsg,
+	     "error in reading Time from %s\n",
+	     c_in_name );
+    return strdup( painCave.errMsg );
+  }
+  time = atof( foo );
 
   // get the Hx vector